* installing *source* package ‘rbamtools’ ... ** package ‘rbamtools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang-trunk/rbamtools/src' /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/bam.c -o samtools/bam.o /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/bam_aux.c -o samtools/bam_aux.o samtools/bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:180:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :309:1: note: expanded from here kh_clear_s ^ samtools/bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:299:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :323:1: note: expanded from here kh_del_s ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function] KHASH_MAP_INIT_STR(r2l, str_p) ^ samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:169:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :330:1: note: expanded from here kh_init_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function] samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:172:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :335:1: note: expanded from here kh_destroy_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function] samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:180:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :338:1: note: expanded from here kh_clear_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function] samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:187:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :341:1: note: expanded from here kh_get_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function] samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:261:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :347:1: note: expanded from here kh_put_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function] samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:299:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :352:1: note: expanded from here kh_del_r2l ^ 8 warnings generated. /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/bam_import.c -o samtools/bam_import.o samtools/bam_import.c:19:1: warning: unused function 'kh_clear_ref' [-Wunused-function] KHASH_MAP_INIT_STR(ref, uint64_t) ^ samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:180:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :304:1: note: expanded from here kh_clear_ref ^ samtools/bam_import.c:19:1: warning: unused function 'kh_get_ref' [-Wunused-function] samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:187:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :307:1: note: expanded from here kh_get_ref ^ samtools/bam_import.c:19:1: warning: unused function 'kh_del_ref' [-Wunused-function] samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:299:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :318:1: note: expanded from here kh_del_ref ^ 3 warnings generated. /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/bam_index.c -o samtools/bam_index.o samtools/bam_index.c:65:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t) ^ samtools/khash.h:498:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:180:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :323:1: note: expanded from here kh_clear_i ^ samtools/bam_index.c:65:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:498:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:299:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :337:1: note: expanded from here kh_del_i ^ 2 warnings generated. /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/bam_sort.c -o samtools/bam_sort.o /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/bgzf.c -o samtools/bgzf.o samtools/bgzf.c:466:24: warning: variable length array folded to constant array as an extension [-Wgnu-folding-constant] bgzf_byte_t header[BLOCK_HEADER_LENGTH]; ^~~~~~~~~~~~~~~~~~~ samtools/bgzf.c:53:1: warning: unused function 'kh_clear_cache' [-Wunused-function] KHASH_MAP_INIT_INT64(cache, cache_t) ^ samtools/khash.h:513:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:180:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :308:1: note: expanded from here kh_clear_cache ^ /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/faidx.c -o samtools/faidx.o samtools/faidx.c:15:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:180:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :308:1: note: expanded from here kh_clear_s ^ samtools/faidx.c:15:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:299:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :322:1: note: expanded from here kh_del_s ^ 2 warnings generated. 2 warnings generated. /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/kstring.c -o samtools/kstring.o /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/razf.c -o samtools/razf.o /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/sam.c -o samtools/sam.o /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -c samtools/sam_header.c -o samtools/sam_header.o samtools/sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, const char *) ^ samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:180:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :306:1: note: expanded from here kh_clear_str ^ samtools/sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function] samtools/khash.h:529:2: 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) ^ samtools/khash.h:309:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static R_INLINE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:299:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :320:1: note: expanded from here kh_del_str ^ 2 warnings generated. /usr/local/clang-trunk/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-trunk/include" -DNDEBUG -isystem /usr/local/clang/include -fpic -g -O3 -Wall -pedantic -frtti -Wno-tautological-overlap-compare -c rbamtools.cpp -o rbamtools.o In file included from rbamtools.cpp:8: In file included from ./rbamtools.h:15: ./extptr.h:110:37: error: no matching function for call to 'Rf_unprotect' virtual ~atmptr() { if(protected_) UNPROTECT(pRob); } ^~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-clang-trunk/include/Rinternals.h:983:22: note: expanded from macro 'UNPROTECT' #define UNPROTECT(n) Rf_unprotect(n) ^~~~~~~~~~~~ /data/gannet/ripley/R/R-clang-trunk/include/Rinternals.h:1750:6: note: candidate function not viable: cannot convert argument of incomplete type 'SEXP' (aka 'SEXPREC *') to 'int' for 1st argument void Rf_unprotect(int); ^ In file included from rbamtools.cpp:8: In file included from ./rbamtools.h:14: ./grange.h:76:11: warning: private field 'last_id' is not used [-Wunused-private-field] unsigned last_id; ^ 1 warning and 1 error generated. make[1]: *** [/data/gannet/ripley/R/R-clang-trunk/etc/Makeconf:173: rbamtools.o] Error 1 make[1]: Target 'all' not remade because of errors. make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang-trunk/rbamtools/src' ERROR: compilation failed for package ‘rbamtools’ * removing ‘/data/gannet/ripley/R/packages/tests-clang-trunk/rbamtools.Rcheck/rbamtools’