##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rbwa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rbwa_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rbwa.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbwa/DESCRIPTION’ ... OK
* this is package ‘Rbwa’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rbwa’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rbwa.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbwa
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘Rbwa’ ...
** using staged installation
** libs
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c utils.c -o utils.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c kthread.c -o kthread.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c kstring.c -o kstring.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c ksw.c -o ksw.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwt.c -o bwt.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bntseq.c -o bntseq.o
bntseq.c:40:1: warning: unused function 'kh_clear_str' [-Wunused-function]
KHASH_MAP_INIT_STR(str, int)
^
./khash.h:612:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
./khash.h:354:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:351:2: note: expanded from macro 'KHASH_INIT2'
        __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:210:13: note: expanded from macro '__KHASH_IMPL'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:85:1: note: expanded from here
kh_clear_str
^
bntseq.c:40:1: warning: unused function 'kh_del_str' [-Wunused-function]
./khash.h:612:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
./khash.h:354:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:351:2: note: expanded from macro 'KHASH_INIT2'
        __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:337:13: note: expanded from macro '__KHASH_IMPL'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:99:1: note: expanded from here
kh_del_str
^
2 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwa.c -o bwa.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwamem.c -o bwamem.o
bwamem.c:213:1: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
KBTREE_INIT(chn, mem_chain_t, chain_cmp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kbtree.h:366:2: note: expanded from macro 'KBTREE_INIT'
        __KB_PUT(name, key_t, __cmp)                            \
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kbtree.h:218:32: note: expanded from macro '__KB_PUT'
                        b->root = s; s->is_internal = 1; s->n = 0;                                      \
                                                    ^ ~
bwamem.c:213:1: warning: unused function 'kb_get_chn' [-Wunused-function]
./kbtree.h:364:2: note: expanded from macro 'KBTREE_INIT'
        __KB_GET(name, key_t)                                           \
        ^
./kbtree.h:146:23: note: expanded from macro '__KB_GET'
        static inline key_t *kb_get_##name(kbtree_##name##_t *b, const key_t k) \
                             ^
<scratch space>:139:1: note: expanded from here
kb_get_chn
^
bwamem.c:213:1: warning: unused function 'kb_interval_chn' [-Wunused-function]
./kbtree.h:365:2: note: expanded from macro 'KBTREE_INIT'
        __KB_INTERVAL(name, key_t)                                      \
        ^
./kbtree.h:169:21: note: expanded from macro '__KB_INTERVAL'
        static inline void kb_interval_##name(kbtree_##name##_t *b, const key_t k, key_t **lower, key_t **upper) \
                           ^
<scratch space>:147:1: note: expanded from here
kb_interval_chn
^
bwamem.c:213:1: warning: unused function 'kb_put_chn' [-Wunused-function]
./kbtree.h:366:2: note: expanded from macro 'KBTREE_INIT'
        __KB_PUT(name, key_t, __cmp)                            \
        ^
./kbtree.h:225:21: note: expanded from macro '__KB_PUT'
        static inline void kb_put_##name(kbtree_##name##_t *b, const key_t k) \
                           ^
<scratch space>:166:1: note: expanded from here
kb_put_chn
^
bwamem.c:213:1: warning: unused function 'kb_del_chn' [-Wunused-function]
./kbtree.h:367:2: note: expanded from macro 'KBTREE_INIT'
        __KB_DEL(name, key_t)
        ^
./kbtree.h:326:22: note: expanded from macro '__KB_DEL'
        static inline key_t kb_del_##name(kbtree_##name##_t *b, const key_t k) \
                            ^
<scratch space>:182:1: note: expanded from here
kb_del_chn
^
5 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwamem_pair.c -o bwamem_pair.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwamem_extra.c -o bwamem_extra.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c malloc_wrap.c -o malloc_wrap.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c QSufSort.c -o QSufSort.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwt_gen.c -o bwt_gen.o
bwt_gen.c:879:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
        bgint_t oldInverseSa0RelativeRank = 0;
                ^
bwt_gen.c:953:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
        unsigned int bitsInWordMinusBitPerChar;
                     ^
2 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c rope.c -o rope.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c rle.c -o rle.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c is.c -o is.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -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
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwashm.c -o bwashm.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwase.c -o bwase.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwtgap.c -o bwtgap.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwtaln.c -o bwtaln.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bamlite.c -o bamlite.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwape.c -o bwape.o
bwape.c:33:1: warning: unused function 'kh_clear_b128' [-Wunused-function]
KHASH_INIT(b128, pair64_t, poslist_t, 1, b128_hash, b128_eq)
^
./khash.h:354:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:351:2: note: expanded from macro 'KHASH_INIT2'
        __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:210:13: note: expanded from macro '__KHASH_IMPL'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:136:1: note: expanded from here
kh_clear_b128
^
bwape.c:33:1: warning: unused function 'kh_get_b128' [-Wunused-function]
./khash.h:354:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:351:2: note: expanded from macro 'KHASH_INIT2'
        __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:217:16: note: expanded from macro '__KHASH_IMPL'
        SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key)        \
                      ^
<scratch space>:139:1: note: expanded from here
kh_get_b128
^
bwape.c:33:1: warning: unused function 'kh_del_b128' [-Wunused-function]
./khash.h:354:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:351:2: note: expanded from macro 'KHASH_INIT2'
        __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:337:13: note: expanded from macro '__KHASH_IMPL'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:150:1: note: expanded from here
kh_del_b128
^
3 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c kopen.c -o kopen.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c pemerge.c -o pemerge.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c maxk.c -o maxk.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o
bwtsw2_core.c:453:45: warning: variable 'n_tot' set but not used [-Wunused-but-set-variable]
        int i, j, score_mat[16], *heap, heap_size, n_tot = 0;
                                                   ^
bwtsw2_core.c:23:1: warning: unused function 'kh_get_qintv' [-Wunused-function]
KHASH_INIT(qintv, qintv_t, uint64_t, 1, qintv_hash, qintv_eq)
^
./khash.h:354:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:351:2: note: expanded from macro 'KHASH_INIT2'
        __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:217:16: note: expanded from macro '__KHASH_IMPL'
        SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key)        \
                      ^
<scratch space>:88:1: note: expanded from here
kh_get_qintv
^
bwtsw2_core.c:23:1: warning: unused function 'kh_del_qintv' [-Wunused-function]
./khash.h:354:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:351:2: note: expanded from macro 'KHASH_INIT2'
        __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:337:13: note: expanded from macro '__KHASH_IMPL'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:99:1: note: expanded from here
kh_del_qintv
^
bwtsw2_core.c:24:1: warning: unused function 'kh_clear_64' [-Wunused-function]
KHASH_MAP_INIT_INT64(64, uint64_t)
^
./khash.h:596:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
        KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
        ^
./khash.h:354:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:351:2: note: expanded from macro 'KHASH_INIT2'
        __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:210:13: note: expanded from macro '__KHASH_IMPL'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:114:1: note: expanded from here
kh_clear_64
^
bwtsw2_core.c:24:1: warning: unused function 'kh_del_64' [-Wunused-function]
./khash.h:596:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
        KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
        ^
./khash.h:354:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:351:2: note: expanded from macro 'KHASH_INIT2'
        __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
./khash.h:337:13: note: expanded from macro '__KHASH_IMPL'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:128:1: note: expanded from here
kh_del_64
^
bwtsw2_core.c:214:22: warning: unused function 'time_elapse' [-Wunused-function]
static inline double time_elapse(const struct rusage *curr, const struct rusage *last)
                     ^
6 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c fastmap.c -o fastmap.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -g -Wall -O2 -c main.c -o main.o
gcc -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
mkdir -p ../inst
cp bwa ../inst/bwa
rm -f gmon.out *.o a.out bwa *~ *.a
rm -f bwa
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rbwa)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Rbwa)
> 
> test_check("Rbwa")
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.02 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa index -p /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f53fb9b69f/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fasta/chr12.fa
[main] Real time: 0.026 sec; CPU: 0.028 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f53fb9b69f/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.005 sec; CPU: 0.006 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f53fb9b69f/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads1.fastq
[main] Real time: 0.007 sec; CPU: 0.006 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f53fb9b69f/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads2.fastq
[main] Real time: 0.005 sec; CPU: 0.006 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.02 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa index -p /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fasta/chr12.fa
[main] Real time: 0.028 sec; CPU: 0.031 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.02 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa index -p /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f55eaba95b/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fasta/chr12.fa
[main] Real time: 0.028 sec; CPU: 0.031 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 7 sequences (133 bp)...
[M::mem_process_seqs] Processed 7 reads in 0.000 CPU sec, 0.000 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa mem /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f55eaba95b/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.001 sec; CPU: 0.002 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 8 sequences (808 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 8 reads in 0.000 CPU sec, 0.000 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa mem /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f55eaba95b/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads1.fastq /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads2.fastq
[main] Real time: 0.001 sec; CPU: 0.002 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.02 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa index -p /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f52b233a00/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fasta/chr12.fa
[main] Real time: 0.028 sec; CPU: 0.031 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f52b233a00/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.005 sec; CPU: 0.006 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f52b233a00/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads1.fastq
[main] Real time: 0.005 sec; CPU: 0.006 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f52b233a00/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads2.fastq
[main] Real time: 0.005 sec; CPU: 0.006 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f52b233a00/chr12 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f52b233a00/output.sai /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.005 sec; CPU: 0.006 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] fail to infer insert size: too few good pairs
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec
[bwa_sai2sam_pe_core] print alignments... 0.00 sec
[bwa_sai2sam_pe_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa sampe /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f52b233a00/chr12 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f52b233a00/output1.sai /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f52b233a00/output2.sai /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads1.fastq /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads2.fastq
[main] Real time: 0.004 sec; CPU: 0.005 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.02 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa index -p /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f5df7f192/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fasta/chr12.fa
[main] Real time: 0.026 sec; CPU: 0.028 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f5df7f192/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.004 sec; CPU: 0.005 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f5df7f192/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads1.fastq
[main] Real time: 0.005 sec; CPU: 0.006 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f5df7f192/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads2.fastq
[main] Real time: 0.004 sec; CPU: 0.005 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f5df7f192/chr12 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f5df7f192/output.sai /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.005 sec; CPU: 0.006 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] fail to infer insert size: too few good pairs
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec
[bwa_sai2sam_pe_core] print alignments... 0.00 sec
[bwa_sai2sam_pe_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa sampe /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f5df7f192/chr12 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f5df7f192/output1.sai /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpviUYgG/file19f5df7f192/output2.sai /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads1.fastq /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/reads/reads2.fastq
[main] Real time: 0.004 sec; CPU: 0.005 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
  0.462   0.138   0.621