Multiple platform build/check report for BioC 3.20 - BUILD BIN results for Rbwa on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD BIN results for Rbwa on lconway

To the developers/maintainers of the Rbwa package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbwa.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: Rbwa

Version: 1.10.0

Command: rm -rf Rbwa.buildbin-libdir && mkdir Rbwa.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbwa_1.10.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rbwa.buildbin-libdir

StartedAt: 2024-11-20 04:45:09 -0500 (Wed, 20 Nov 2024)

EndedAt: 2024-11-20 04:45:40 -0500 (Wed, 20 Nov 2024)

EllapsedTime: 30.3 seconds

RetCode: 0

Status: OK

PackageFile: Rbwa_1.10.0.tgz

PackageFileSize: 650.9 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rbwa.buildbin-libdir && mkdir Rbwa.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbwa_1.10.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rbwa.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rbwa.buildbin-libdir Rbwa_1.10.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Rbwa’ ...
** using staged installation
rm -f gmon.out *.o a.out bwa *~ *.a
rm -f bwa
** libs
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c utils.c -o utils.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c kthread.c -o kthread.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c kstring.c -o kstring.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c ksw.c -o ksw.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c bwt.c -o bwt.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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>:84:1: 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>:98:1: note: expanded from here
kh_del_str
^
2 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c bwa.c -o bwa.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c bwamem.c -o bwamem.o
bwamem.c:213:1: warning: unused function 'kb_get_chn' [-Wunused-function]
KBTREE_INIT(chn, mem_chain_t, chain_cmp)
^
./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>:33:1: 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>:41:1: 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>:60:1: 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>:76:1: note: expanded from here
kb_del_chn
^
4 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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/x86_64/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/x86_64/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/x86_64/include    -fPIC  -g -Wall -O2 -c QSufSort.c -o QSufSort.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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/x86_64/include    -fPIC  -g -Wall -O2 -c rope.c -o rope.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c rle.c -o rle.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c is.c -o is.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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/x86_64/include    -fPIC  -g -Wall -O2 -c bwashm.c -o bwashm.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c bwase.c -o bwase.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c bwtgap.c -o bwtgap.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c bwtaln.c -o bwtaln.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c bamlite.c -o bamlite.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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>:22:1: 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>:25:1: 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>:36:1: note: expanded from here
kh_del_b128
^
3 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c kopen.c -o kopen.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c pemerge.c -o pemerge.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -g -Wall -O2 -c maxk.c -o maxk.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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>:87:1: 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>:98:1: 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>:113:1: 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>:127:1: 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/x86_64/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/x86_64/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/x86_64/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/x86_64/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/x86_64/include    -fPIC  -g -Wall -O2 -c fastmap.c -o fastmap.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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/x86_64/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)