>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ShortRead.buildbin-libdir ShortRead_1.18.0.tar.gz'
>>>>>>>
* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_ShortRead.c -o R_init_ShortRead.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c alphabet.c -o alphabet.o
alphabet.c:31:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ansp, 0, LENGTH(ans) * sizeof(int)); /* initialize to 0 */
^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
alphabet.c:31:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ansp, 0, LENGTH(ans) * sizeof(int)); /* initialize to 0 */
^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
alphabet.c:39:13: warning: variable length array folded to constant array as an extension [-Wpedantic]
int map[MAX_MAP];
^˜˜˜˜˜˜
alphabet.c:96:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ansp, 0, LENGTH(ans) * sizeof(int)); /* initialize to 0 */
^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
alphabet.c:96:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ansp, 0, LENGTH(ans) * sizeof(int)); /* initialize to 0 */
^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
alphabet.c:106:14: warning: variable length array folded to constant array as an extension [-Wpedantic]
int map1[MAX_MAP], map2[MAX_MAP];
^˜˜˜˜˜˜
alphabet.c:106:29: warning: variable length array folded to constant array as an extension [-Wpedantic]
int map1[MAX_MAP], map2[MAX_MAP];
^˜˜˜˜˜˜
alphabet.c:232:32: warning: operand of ? changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t len = diff < 0 ? ra.length : rb.length;
˜˜˜ ˜˜˜^˜˜˜˜˜
alphabet.c:232:44: warning: operand of ? changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t len = diff < 0 ? ra.length : rb.length;
˜˜˜ ˜˜˜^˜˜˜˜˜
alphabet.c:243:32: warning: operand of ? changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t len = diff < 0 ? ra.length : rb.length;
˜˜˜ ˜˜˜^˜˜˜˜˜
alphabet.c:243:44: warning: operand of ? changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t len = diff < 0 ? ra.length : rb.length;
˜˜˜ ˜˜˜^˜˜˜˜˜
alphabet.c:258:17: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(xptr, len, sizeof(XSort), stable_compare_cachedCharSeq);
˜˜˜˜˜ ^˜˜
alphabet.c:268:37: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
XSort *xptr = (XSort *) R_alloc(len, sizeof(XSort));
˜˜˜˜˜˜˜ ^˜˜
alphabet.c:288:37: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
XSort *xptr = (XSort *) R_alloc(len, sizeof(XSort));
˜˜˜˜˜˜˜ ^˜˜
alphabet.c:311:37: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
XSort *xptr = (XSort *) R_alloc(len, sizeof(XSort));
˜˜˜˜˜˜˜ ^˜˜
15 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c io.c -o io.o
io.c:39:22: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
buf[j] = decode(roSeq.seq[j]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:111:14: warning: variable length array folded to constant array as an extension [-Wpedantic]
char buf[LINEBUF_SIZE + 1];
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:115:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while (*n_cycles == 0 && (bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:117:56: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while ((p = memchr(p, '\n', (buf + bytes_read) - p))) {
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
io.c:128:57: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while ((p = memchr(p, CYCLE_END, (buf + bytes_read) - p))) {
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
io.c:132:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while ((bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:134:61: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while ((p = memchr(p, CYCLE_END, (buf + bytes_read) - p))) {
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
io.c:224:36: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
score[cycle++] = qbase + ((char) v[0] > v[2] ? v[0] : v[2]);
˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:550:38: warning: variable length array folded to constant array as an extension [-Wpedantic]
char linebuf[LINEBUF_SIZE], *elt[N_FIELDS];
^˜˜˜˜˜˜˜
io.c:713:18: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
withId = LOGICAL(withFlags)[0],
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:714:30: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
withMultiplexIndex = LOGICAL(withFlags)[1],
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:715:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
withPairedReadNumber = LOGICAL(withFlags)[2];
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c io_bowtie.c -o io_bowtie.o
io_bowtie.c:21:38: warning: variable length array folded to constant array as an extension [-Wpedantic]
char linebuf[LINEBUF_SIZE], *elt[N_FIELDS];
^˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c io_soap.c -o io_soap.o
io_soap.c:22:38: warning: variable length array folded to constant array as an extension [-Wpedantic]
char linebuf[LINEBUF_SIZE], *elt[N_FIELDS];
^˜˜˜˜˜˜˜
io_soap.c:22:38: note: initializer of 'N_FIELDS' is not a constant expression
io_soap.c:20:15: note: declared here
const int N_FIELDS = N_ELTS;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c pileup.c -o pileup.o
pileup.c:13:29: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(res), 0, length(res) * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1029:20: note: expanded from macro 'length'
#define length(x) Rf_length(x)
^˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
pileup.c:13:29: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(res), 0, length(res) * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1029:20: note: expanded from macro 'length'
#define length(x) Rf_length(x)
^˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc:35:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
(void) fread( seq_name, sizeof(char), name_len, fp );
˜˜˜˜˜ ^˜˜˜˜˜˜˜
readBfaToc.cc:41:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
fseek( fp, 2 * sizeof(bit64_t) * seq_len, SEEK_CUR);
˜ ^˜˜˜˜˜˜
readBfaToc.cc:47:40: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT( res = allocVector( INTSXP, seqs.size() ) );
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
readBfaToc.cc:48:42: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT( names = allocVector( STRSXP, seqs.size() ) );
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c read_maq_map.cc -o read_maq_map.o
read_maq_map.cc:128:41: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
INTEGER(seq )[i] = read.seqid + 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
read_maq_map.cc:180:14: note: in instantiation of function template specialization 'read_maq_map_B<128>' requested here
return read_maq_map_B< MAX_READLEN_NEW >( filename, maxreads );
^
read_maq_map.cc:80:32: warning: implicit conversion loses integer precision: 'bit64_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
actnreads = mapheader->n_mapped_reads;
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from read_maq_map.cc:13:
./maqmap_m.h:106:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mm->ref_name = (char **) calloc(mm->n_ref, sizeof(char *));
˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
read_maq_map.cc:73:18: note: in instantiation of function template specialization 'maqmap_read_header<128>' requested here
mapheader = maqmap_read_header<max_readlen>( mapfile );
^
read_maq_map.cc:180:14: note: in instantiation of function template specialization 'read_maq_map_B<128>' requested here
return read_maq_map_B< MAX_READLEN_NEW >( filename, maxreads );
^
In file included from read_maq_map.cc:13:
./maqmap_m.h:109:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mm->ref_name[k] = (char *) malloc(len * sizeof(char));
^˜˜ ˜
./maqmap_m.h:110:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gzread(fp, mm->ref_name[k], len);
˜˜˜˜˜˜ ^˜˜
read_maq_map.cc:128:41: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
INTEGER(seq )[i] = read.seqid + 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
read_maq_map.cc:182:14: note: in instantiation of function template specialization 'read_maq_map_B<64>' requested here
return read_maq_map_B< MAX_READLEN_OLD >( filename, maxreads );
^
read_maq_map.cc:80:32: warning: implicit conversion loses integer precision: 'bit64_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
actnreads = mapheader->n_mapped_reads;
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from read_maq_map.cc:13:
./maqmap_m.h:106:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mm->ref_name = (char **) calloc(mm->n_ref, sizeof(char *));
˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
read_maq_map.cc:73:18: note: in instantiation of function template specialization 'maqmap_read_header<64>' requested here
mapheader = maqmap_read_header<max_readlen>( mapfile );
^
read_maq_map.cc:182:14: note: in instantiation of function template specialization 'read_maq_map_B<64>' requested here
return read_maq_map_B< MAX_READLEN_OLD >( filename, maxreads );
^
In file included from read_maq_map.cc:13:
./maqmap_m.h:109:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mm->ref_name[k] = (char *) malloc(len * sizeof(char));
^˜˜ ˜
./maqmap_m.h:110:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gzread(fp, mm->ref_name[k], len);
˜˜˜˜˜˜ ^˜˜
10 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sampler.c -o sampler.o
sampler.c:135:44: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memcpy((char *) x.seq, start, (buf - start) * sizeof(Rbyte));
˜˜˜˜^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:135:44: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memcpy((char *) x.seq, start, (buf - start) * sizeof(Rbyte));
˜˜˜˜^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:143:37: warning: implicit conversion changes signedness: 'const Rbyte' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
*curr++ = DNAencode(*buf++);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
sampler.c:159:27: warning: implicit conversion changes signedness: 'const Rbyte' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
*curr++ = *buf++;
˜ ^˜˜˜˜˜
sampler.c:92:23: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
id_w[i] = buf - start;
˜ ˜˜˜˜^˜˜˜˜˜˜
sampler.c:232:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(intern_record, record, len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:232:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(intern_record, record, len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:245:25: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
int j = (n - i) * unif_rand();
˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
sampler.c:259:18: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
int n_samp = rbinom(n_curr, n_choose / n_tot);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:312:17: note: expanded from macro 'rbinom'
#define rbinom Rf_rbinom
^
sampler.c:299:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(sample->records, sample->n_curr,
˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜
sampler.c:310:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(bytes, record, len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:310:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(bytes, record, len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:348:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buf, scratch->bytes, scratch->len * sizeof(Rbyte));
˜˜˜˜˜˜˜˜˜^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:348:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buf, scratch->bytes, scratch->len * sizeof(Rbyte));
˜˜˜˜˜˜˜˜˜^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:350:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buf + scratch->len, RAW(bin), len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:350:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buf + scratch->len, RAW(bin), len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:356:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buf, RAW(bin), buflen * sizeof(Rbyte));
^˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:356:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buf, RAW(bin), buflen * sizeof(Rbyte));
^˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:380:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(tail, buf, len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:380:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(tail, buf, len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:372:41: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
_sampler_add(sampler, prev, buf - prev);
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
sampler.c:378:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int len = bufend - buf;
˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜
sampler.c:500:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(scratch->bytes, RAW(bin), len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:500:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(scratch->bytes, RAW(bin), len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:505:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(bytes, scratch->bytes, buflen * sizeof(Rbyte));
^˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:505:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(bytes, scratch->bytes, buflen * sizeof(Rbyte));
^˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:506:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(bytes + buflen, RAW(bin), len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:506:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(bytes + buflen, RAW(bin), len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:540:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(tail, buf, len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sampler.c:540:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(tail, buf, len * sizeof(Rbyte));
^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sampler.c:526:45: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
_streamer_add(stream, prev, buf - prev);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
sampler.c:538:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int len = bufend - buf;
˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜
32 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c trim.c -o trim.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c util.c -o util.o
util.c:257:25: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
i = strlen(linebuf) - 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
util.c:281:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tmp = linebuf[len - i - 1];
˜ ^
util.c:282:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
linebuf[len - i - 1] = linebuf[i];
˜ ^
util.c:342:14: warning: variable length array folded to constant array as an extension [-Wpedantic]
char buf[LINEBUF_SIZE + 1];
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
util.c:345:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while ((bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
util.c:347:56: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while ((p = memchr(p, '\n', (buf + bytes_read) - p))) {
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c xsnap.c -o xsnap.o
xsnap.c:70:29: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int offset = node->curr - node->buf;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
xsnap.c:82:34: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
const int n_raw = node->curr - node->buf;
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
xsnap.c:93:24: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
node->curr - (node->buf + offset[node->n - 1]);
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xsnap.c:127:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int w = strlen(s);
˜ ^˜˜˜˜˜˜˜˜
4 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ShortRead)
>>>>>>>
>>>>>>> FIXING LINKS FOR ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so"