VariantAnnotation 1.6.5
Valerie Obenchain
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/VariantAnnotation | | Last Changed Rev: 75841 / Revision: 76155 | | Last Changed Date: 2013-04-20 11:42:29 -0700 (Sat, 20 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.6.5.tar.gz'
>>>>>>>
* installing *source* package 'VariantAnnotation' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
In file included from R_init_VariantAnnotation.c:2:
In file included from ./vcffile.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/tabix.h:32:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c dna_hash.c -o dna_hash.o
In file included from dna_hash.c:7:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
dna_hash.c:42:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
dna->offset = Realloc(dna->offset, size, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
dna_hash.c:59:37: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
dna_hash_grow(dna, DNA_GROW * dna->size);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
dna_hash.c:97:23: warning: implicit conversion changes signedness: 'char' to 'Rbyte' (aka 'unsigned char') [-Wsign-conversion]
*tagp++ = DNAencode(cstr[j]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dna_hash.c:82:42: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
iwidth[idx] = '.' == *cstr ? 0 : strlen(cstr);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c rle.c -o rle.o
rle.c:29:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rle->value = Realloc(rle->value, size, char *);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
rle.c:30:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rle->length = Realloc(rle->length, size, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
rle.c:39:36: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
rle_grow(rle, RLE_GROW * rle->size);
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c utilities.c -o utilities.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c vcffile.c -o vcffile.o
In file included from vcffile.c:2:
In file included from ./vcffile.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/tabix.h:32:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/tabix/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
In file included from vcffile.c:8:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
vcffile.c:68:29: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
SEXPTYPE type = TYPEOF(VECTOR_ELT(map, j));
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
vcffile.c:119:25: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
SEXPTYPE type = TYPEOF(VECTOR_ELT(fmap, i));
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
vcffile.c:362:52: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
size = parse->vcf_n < 2 ? 2 : parse->vcf_n * SCALE;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
vcffile.c:416:54: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
const int len0 = end - buf0, len1 = len0 * 1.6;
˜˜˜˜ ˜˜˜˜˜^˜˜˜˜
vcffile.c:417:34: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
buf0 = Realloc(buf0, len1, char);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
vcffile.c:413:42: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
while (Z_NULL != gzgets(gz, buf, end - buf)) {
˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
vcffile.c:414:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int n = strlen(buf);
˜ ^˜˜˜˜˜˜˜˜˜˜
vcffile.c:416:34: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
const int len0 = end - buf0, len1 = len0 * 1.6;
˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
vcffile.c:431:32: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int last = strlen(buf) - 1;
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
22 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c vcftype.c -o vcftype.o
vcftype.c:71:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vcf_Realloc(vcftype->u.logical, sz * sizeof(int));
^˜ ˜
vcftype.c:77:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vcf_Realloc(vcftype->u.integer, sz * sizeof(int));
^˜ ˜
vcftype.c:83:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vcf_Realloc(vcftype->u.numeric, sz * sizeof(double));
^˜ ˜
vcftype.c:89:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vcf_Realloc(vcftype->u.character, sz * sizeof(char *));
^˜ ˜
vcftype.c:95:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vcf_Realloc(vcftype->u.list, sz * sizeof(struct vcftype_t *));
^˜ ˜
5 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 VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o dna_hash.o rle.o utilities.o vcffile.o vcftype.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-2.12-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/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 (VariantAnnotation)
>>>>>>>
>>>>>>> FIXING LINKS FOR VariantAnnotation.buildbin-libdir/VariantAnnotation/libs//VariantAnnotation.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" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs//VariantAnnotation.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs//VariantAnnotation.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" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs//VariantAnnotation.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs//VariantAnnotation.so"