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Package 450/671HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.24.0
Benilton Carvalho
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/oligo
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 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 ]

Summary

Package: oligo
Version: 1.24.0
Command: rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.24.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R oligo.buildbin-libdir
StartedAt: 2013-05-01 12:41:20 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:41:48 -0700 (Wed, 01 May 2013)
EllapsedTime: 27.8 seconds
RetCode: 0
Status:  OK 
PackageFile: oligo_1.24.0.tgz
PackageFileSize: 5.441 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=oligo.buildbin-libdir oligo_1.24.0.tar.gz'
>>>>>>> 

* installing *source* package 'oligo' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c DABG.c -o DABG.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c:53:21: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
  j = strlen(buffer)-1;
    ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ParserGzXYS.c:90:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    j = strlen(buffer)-1;
      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
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/preprocessCore/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ParserXYS.c -o ParserXYS.o
ParserXYS.c:47:52: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    while ((p = memchr(p, '\n', (buf + bytes_read) - p))) {
                ˜˜˜˜˜˜          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
ParserXYS.c:77:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  header->key = Realloc(header->key, header->n, 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)) )
                                                                   ^
ParserXYS.c:78:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  header->value = Realloc(header->value, header->n, 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)) )
                                                                   ^
ParserXYS.c:148:21: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
  j = strlen(buffer)-1;
    ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ParserXYS.c:189:14: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        xy[count] = strtol(sx, &endpx, 0);
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ParserXYS.c:190:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        xy[count + nrow] = strtol(sy, &endpy, 0);
                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ParserXYS.c:323:21: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
  j = strlen(buffer)-1;
    ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
7 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/preprocessCore/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c baseProfile.c -o baseProfile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c basecontent.c -o basecontent.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c chipbackground.c -o chipbackground.o
chipbackground.c:379:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(data_by_sector[j],cur_n[j],sizeof(double),(int(*)(const void*, const void*))sort_double);
    ˜˜˜˜˜                   ^˜˜˜˜˜˜˜
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/preprocessCore/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mas5calls.c -o mas5calls.o
mas5calls.c:96:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
  r      = (double *) R_alloc(nx,sizeof(double));
                      ˜˜˜˜˜˜˜ ^˜
mas5calls.c:97:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
  absx   = (double *) R_alloc(nx,sizeof(double));
                      ˜˜˜˜˜˜˜ ^˜
mas5calls.c:98:28: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
  xidx   = (int *) R_alloc(nx,sizeof(int));
                   ˜˜˜˜˜˜˜ ^˜
mas5calls.c:104:30: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  rsort_with_index(absx,xidx,nx);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜
mas5calls.c:105:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  rank(absx,nx,r);
  ˜˜˜˜      ^˜
mas5calls.c:151:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    ignore = (int *) R_alloc(n, sizeof(int));
                     ˜˜˜˜˜˜˜ ^
mas5calls.c:175:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  dv = (double *) R_alloc(n, sizeof(double));
                  ˜˜˜˜˜˜˜ ^
7 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/preprocessCore/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c rma2.c -o rma2.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c rma_common.c -o rma_common.o
rma_common.c:64:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memcpy(buffer,x,length*sizeof(double));
                  ^˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
rma_common.c:64:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memcpy(buffer,x,length*sizeof(double));
                  ^˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
rma_common.c:106:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memcpy(buffer,x,length*sizeof(double));
                  ^˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
rma_common.c:106:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memcpy(buffer,x,length*sizeof(double));
                  ^˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
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/preprocessCore/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c trimmed.c -o trimmed.o
trimmed.c:29:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  qsort(buffer, n, sizeof(double), (int(*)(const void*, const void*))sort_double);
  ˜˜˜˜˜         ^
1 warning 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 oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/oligo.buildbin-libdir/oligo/libs
** R
** inst
** preparing package for lazy loading
Note: in method for 'pm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for 'mm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligo)


>>>>>>> 
>>>>>>> FIXING LINKS FOR oligo.buildbin-libdir/oligo/libs//oligo.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" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.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" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"