+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/local/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-fastmatch-1.1.6/work.log + su pbulk -c '"$@"' make /opt/local/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-fastmatch-1.1.6/work.log ===> Installing for R-fastmatch-1.1.6 => Generating pre-install file lists => Creating installation directories * installing *source* package 'fastmatch' ... ** this is package 'fastmatch' version '1.1-6' ** package 'fastmatch' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (GCC) 13.4.0' gcc -std=gnu2x -I"/opt/local/lib/R/include" -DNDEBUG -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED -I/opt/local/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED -I/opt/local/include/libxml2 -c ctapply.c -o ctapply.o ctapply.c: In function 'ctapply_': ctapply.c:42:13: warning: implicit declaration of function 'SET_NAMED' [-Wimplicit-function-declaration] 42 | SET_NAMED(cdi = SET_VECTOR_ELT(tmp, 0, allocVector(TYPEOF(by), (cdlen = ((N < MIN_CACHE) ? MIN_CACHE : N)))), 1); | ^~~~~~~~~ ctapply.c:48:9: warning: implicit declaration of function 'SETLENGTH'; did you mean 'XLENGTH'? [-Wimplicit-function-declaration] 48 | SETLENGTH(cdi, N); | ^~~~~~~~~ | XLENGTH ctapply.c:53:47: warning: implicit declaration of function 'STRING_PTR'; did you mean 'STRING_ELT'? [-Wimplicit-function-declaration] 53 | else if (TYPEOF(by) == STRSXP) memcpy(STRING_PTR(cdi), STRING_PTR(by) + i0, sizeof(SEXP) * N); | ^~~~~~~~~~ | STRING_ELT ctapply.c:53:47: warning: passing argument 1 of 'memcpy' makes pointer from integer without a cast [-Wint-conversion] 53 | else if (TYPEOF(by) == STRSXP) memcpy(STRING_PTR(cdi), STRING_PTR(by) + i0, sizeof(SEXP) * N); | ^~~~~~~~~~~~~~~ | | | int In file included from /usr/include/string.h:34, from ctapply.c:2: /usr/include/iso/string_iso.h:70:21: note: expected 'void * restrict' but argument is of type 'int' 70 | extern void *memcpy(void *_RESTRICT_KYWD, const void *_RESTRICT_KYWD, size_t); | ^ ctapply.c:53:79: warning: passing argument 2 of 'memcpy' makes pointer from integer without a cast [-Wint-conversion] 53 | else if (TYPEOF(by) == STRSXP) memcpy(STRING_PTR(cdi), STRING_PTR(by) + i0, sizeof(SEXP) * N); | ~~~~~~~~~~~~~~~^~~~ | | | int /usr/include/iso/string_iso.h:70:43: note: expected 'const void * restrict' but argument is of type 'int' 70 | extern void *memcpy(void *_RESTRICT_KYWD, const void *_RESTRICT_KYWD, size_t); | ^ ctapply.c:57:48: warning: passing argument 1 of 'memcpy' makes pointer from integer without a cast [-Wint-conversion] 57 | else if (TYPEOF(vec) == STRSXP) memcpy(STRING_PTR(cdv), STRING_PTR(vec) + i0, sizeof(SEXP) * N); | ^~~~~~~~~~~~~~~ | | | int /usr/include/iso/string_iso.h:70:21: note: expected 'void * restrict' but argument is of type 'int' 70 | extern void *memcpy(void *_RESTRICT_KYWD, const void *_RESTRICT_KYWD, size_t); | ^ ctapply.c:57:81: warning: passing argument 2 of 'memcpy' makes pointer from integer without a cast [-Wint-conversion] 57 | else if (TYPEOF(vec) == STRSXP) memcpy(STRING_PTR(cdv), STRING_PTR(vec) + i0, sizeof(SEXP) * N); | ~~~~~~~~~~~~~~~~^~~~ | | | int /usr/include/iso/string_iso.h:70:43: note: expected 'const void * restrict' but argument is of type 'int' 70 | extern void *memcpy(void *_RESTRICT_KYWD, const void *_RESTRICT_KYWD, size_t); | ^ ctapply.c:58:48: warning: implicit declaration of function 'VECTOR_PTR'; did you mean 'VECTOR_PTR_RO'? [-Wimplicit-function-declaration] 58 | else if (TYPEOF(vec) == VECSXP) memcpy(VECTOR_PTR(cdv), VECTOR_PTR(vec) + i0, sizeof(SEXP) * N); | ^~~~~~~~~~ | VECTOR_PTR_RO ctapply.c:58:48: warning: passing argument 1 of 'memcpy' makes pointer from integer without a cast [-Wint-conversion] 58 | else if (TYPEOF(vec) == VECSXP) memcpy(VECTOR_PTR(cdv), VECTOR_PTR(vec) + i0, sizeof(SEXP) * N); | ^~~~~~~~~~~~~~~ | | | int /usr/include/iso/string_iso.h:70:21: note: expected 'void * restrict' but argument is of type 'int' 70 | extern void *memcpy(void *_RESTRICT_KYWD, const void *_RESTRICT_KYWD, size_t); | ^ ctapply.c:58:81: warning: passing argument 2 of 'memcpy' makes pointer from integer without a cast [-Wint-conversion] 58 | else if (TYPEOF(vec) == VECSXP) memcpy(VECTOR_PTR(cdv), VECTOR_PTR(vec) + i0, sizeof(SEXP) * N); | ~~~~~~~~~~~~~~~~^~~~ | | | int /usr/include/iso/string_iso.h:70:43: note: expected 'const void * restrict' but argument is of type 'int' 70 | extern void *memcpy(void *_RESTRICT_KYWD, const void *_RESTRICT_KYWD, size_t); | ^ ctapply.c:69:13: warning: implicit declaration of function 'NAMED' [-Wimplicit-function-declaration] 69 | if (NAMED(eres) > 1) eres = duplicate(eres); | ^~~~~ gcc -std=gnu2x -I"/opt/local/lib/R/include" -DNDEBUG -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED -I/opt/local/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED -I/opt/local/include/libxml2 -c dummy.c -o dummy.o gcc -std=gnu2x -I"/opt/local/lib/R/include" -DNDEBUG -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED -I/opt/local/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED -I/opt/local/include/libxml2 -c fasthash.c -o fasthash.o fasthash.c: In function 'new_hash': fasthash.c:65:14: warning: implicit declaration of function 'DATAPTR'; did you mean 'DATAPTR_RO'? [-Wimplicit-function-declaration] 65 | h->src = DATAPTR(h->parent); | ^~~~~~~ | DATAPTR_RO fasthash.c:65:12: warning: assignment to 'void *' from 'int' makes pointer from integer without a cast [-Wint-conversion] 65 | h->src = DATAPTR(h->parent); | ^ fasthash.c: In function 'hash_fin': fasthash.c:80:27: warning: implicit declaration of function 'EXTPTR_PTR' [-Wimplicit-function-declaration] 80 | hash_t *h = (hash_t*) EXTPTR_PTR(ho); | ^~~~~~~~~~ fasthash.c:80:17: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 80 | hash_t *h = (hash_t*) EXTPTR_PTR(ho); | ^ fasthash.c: In function 'append_hash': fasthash.c:268:20: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 268 | SEXP *sv = (SEXP*) DATAPTR(x); | ^ fasthash.c: In function 'unwrap': fasthash.c:285:9: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 285 | h = (hash_t*) EXTPTR_PTR(ht); | ^ fasthash.c: In function 'mk_hash': fasthash.c:340:9: warning: implicit declaration of function 'OBJECT' [-Wimplicit-function-declaration] 340 | if (OBJECT(x)) { | ^~~~~~ fasthash.c: In function 'get_table': fasthash.c:429:12: warning: passing argument 1 of 'memcpy' makes pointer from integer without a cast [-Wint-conversion] 429 | memcpy(DATAPTR(res), DATAPTR(h->parent), sz); | ^~~~~~~~~~~~ | | | int In file included from /usr/include/string.h:34, from fasthash.c:26: /usr/include/iso/string_iso.h:70:21: note: expected 'void * restrict' but argument is of type 'int' 70 | extern void *memcpy(void *_RESTRICT_KYWD, const void *_RESTRICT_KYWD, size_t); | ^ fasthash.c:429:26: warning: passing argument 2 of 'memcpy' makes pointer from integer without a cast [-Wint-conversion] 429 | memcpy(DATAPTR(res), DATAPTR(h->parent), sz); | ^~~~~~~~~~~~~~~~~~ | | | int /usr/include/iso/string_iso.h:70:43: note: expected 'const void * restrict' but argument is of type 'int' 70 | extern void *memcpy(void *_RESTRICT_KYWD, const void *_RESTRICT_KYWD, size_t); | ^ fasthash.c: In function 'get_values': fasthash.c:474:24: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 474 | SEXP *rv = (SEXP*) DATAPTR(x); | ^ gcc -std=gnu2x -I"/opt/local/lib/R/include" -DNDEBUG -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED -I/opt/local/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED -I/opt/local/include/libxml2 -c fastmatch.c -o fastmatch.o fastmatch.c: In function 'hash_fin': fastmatch.c:76:25: warning: implicit declaration of function 'EXTPTR_PTR' [-Wimplicit-function-declaration] 76 | hash_t *h = (hash_t*) EXTPTR_PTR(ho); | ^~~~~~~~~~ fastmatch.c:76:15: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 76 | hash_t *h = (hash_t*) EXTPTR_PTR(ho); | ^ fastmatch.c: In function 'fmatch': fastmatch.c:263:9: warning: implicit declaration of function 'OBJECT' [-Wimplicit-function-declaration] 263 | if (OBJECT(x)) { | ^~~~~~ fastmatch.c:304:13: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 304 | h = (hash_t*) EXTPTR_PTR(a); | ^ fastmatch.c:322:22: warning: implicit declaration of function 'DATAPTR'; did you mean 'DATAPTR_RO'? [-Wimplicit-function-declaration] 322 | h = new_hash(DATAPTR(y), XLENGTH(y)); | ^~~~~~~ | DATAPTR_RO fastmatch.c:322:22: warning: passing argument 1 of 'new_hash' makes pointer from integer without a cast [-Wint-conversion] 322 | h = new_hash(DATAPTR(y), XLENGTH(y)); | ^~~~~~~~~~ | | | int fastmatch.c:54:31: note: expected 'void *' but argument is of type 'int' 54 | static hash_t *new_hash(void *src, hash_index_t len) { | ~~~~~~^~~ fastmatch.c:334:26: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 334 | hash_t *lh = (hash_t*) EXTPTR_PTR(a); | ^ fastmatch.c:351:20: warning: assignment to 'void *' from 'int' makes pointer from integer without a cast [-Wint-conversion] 351 | h->src = DATAPTR(y); /* this is ugly, but we need to adjust the source since we changed it */ | ^ fastmatch.c:419:31: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 419 | SEXP *k = (SEXP*) DATAPTR(x); | ^ fastmatch.c:433:31: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 433 | SEXP *k = (SEXP*) DATAPTR(x); | ^ fastmatch.c:453:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 453 | SEXP *k = (SEXP*) DATAPTR(x); | ^ fastmatch.c: In function 'coalesce': fastmatch.c:473:18: warning: passing argument 1 of 'new_hash' makes pointer from integer without a cast [-Wint-conversion] 473 | h = new_hash(DATAPTR(x), XLENGTH(x)); | ^~~~~~~~~~ | | | int fastmatch.c:54:31: note: expected 'void *' but argument is of type 'int' 54 | static hash_t *new_hash(void *src, hash_index_t len) { | ~~~~~~^~~ gcc -std=gnu2x -shared -L/opt/local/lib/R/lib -Wl,-R/opt/local/lib/R/lib -L/opt/local/lib -Wl,-R/opt/local/lib -liconv -lintl -pthread -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -o fastmatch.so ctapply.o dummy.o fasthash.o fastmatch.o -L/opt/local/lib/R/lib installing to /home/pbulk/build/math/R-fastmatch/work/.destdir/opt/local/lib/R/library/00LOCK-fastmatch/00new/fastmatch/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for 'fastmatch' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/pbulk/build/math/R-fastmatch/work/.destdir/opt/local/lib/R/library/00LOCK-fastmatch/00new/fastmatch/libs/fastmatch.so': ld.so.1: R: fatal: relocation error: file /home/pbulk/build/math/R-fastmatch/work/.destdir/opt/local/lib/R/library/00LOCK-fastmatch/00new/fastmatch/libs/fastmatch.so: symbol SETLENGTH: referenced symbol not found Error: loading failed Execution halted ERROR: loading failed * removing '/home/pbulk/build/math/R-fastmatch/work/.destdir/opt/local/lib/R/library/fastmatch' *** Error code 1 Stop. bmake[1]: stopped making "stage-install" in /data/jenkins/workspace/pkgsrc-trunk-x86_64/math/R-fastmatch *** Error code 1 Stop. bmake: stopped making "stage-install" in /data/jenkins/workspace/pkgsrc-trunk-x86_64/math/R-fastmatch