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Package 625/671HostnameOS / ArchBUILDCHECKBUILD BIN
Starr 1.16.0
Benedikt Zacher
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/Starr
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: Starr
Version: 1.16.0
Command: rm -rf Starr.buildbin-libdir && mkdir Starr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Starr_1.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Starr.buildbin-libdir
StartedAt: 2013-05-01 12:57:33 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:58:06 -0700 (Wed, 01 May 2013)
EllapsedTime: 32.3 seconds
RetCode: 0
Status:  OK 
PackageFile: Starr_1.16.0.tgz
PackageFileSize: 1.713 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Starr.buildbin-libdir Starr_1.16.0.tar.gz'
>>>>>>> 

* installing *source* package 'Starr' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ahocorasick.c -o ahocorasick.o
ahocorasick.c:8:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:218:2: note: expanded from macro 'KSEQ_INIT'
        KSTREAM_INIT(type_t, __read, 4096)                      \
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:143:2: note: expanded from macro 'KSTREAM_INIT'
        __KS_GETUNTIL(__read, __bufsize)
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:119:26: note: expanded from macro '__KS_GETUNTIL'
                                str->m = str->l + (i - ks->begin) + 1;                                  \
                                                ˜  ˜˜^˜˜˜˜˜˜˜˜˜˜
ahocorasick.c:8:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:218:2: note: expanded from macro 'KSEQ_INIT'
        KSTREAM_INIT(type_t, __read, 4096)                      \
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:143:2: note: expanded from macro 'KSTREAM_INIT'
        __KS_GETUNTIL(__read, __bufsize)
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:124:25: note: expanded from macro '__KS_GETUNTIL'
                        str->l = str->l + (i - ks->begin);                                                      \
                                        ˜  ˜˜^˜˜˜˜˜˜˜˜˜˜
ahocorasick.c:8:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:218:2: note: expanded from macro 'KSEQ_INIT'
        KSTREAM_INIT(type_t, __read, 4096)                      \
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:143:2: note: expanded from macro 'KSTREAM_INIT'
        __KS_GETUNTIL(__read, __bufsize)
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:136:15: note: expanded from macro '__KS_GETUNTIL'
                return str->l;                                                                                                  \
                ˜˜˜˜˜˜ ˜˜˜˜˜^
ahocorasick.c:8:1: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:221:2: note: expanded from macro 'KSEQ_INIT'
        __KSEQ_READ
        ^˜˜˜˜˜˜˜˜˜˜
./kseq.h:203:58: note: expanded from macro '__KSEQ_READ'
                        if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
                                                                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ahocorasick.c:8:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:221:2: note: expanded from macro 'KSEQ_INIT'
        __KSEQ_READ
        ^˜˜˜˜˜˜˜˜˜˜
./kseq.h:195:33: note: expanded from macro '__KSEQ_READ'
                if (c != '+') return seq->seq.l; /* FASTA */                                    \
                              ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^
ahocorasick.c:8:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:221:2: note: expanded from macro 'KSEQ_INIT'
        __KSEQ_READ
        ^˜˜˜˜˜˜˜˜˜˜
./kseq.h:207:19: note: expanded from macro '__KSEQ_READ'
                return seq->seq.l;                                                                                              \
                ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^
ahocorasick.c:233:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  nodep *queue = (nodep *)malloc(sizeof(nodep)*num_nodes);
                                              ˜^˜˜˜˜˜˜˜˜
ahocorasick.c:350:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  int *wlens = (int*)malloc(INTEGER(wcount_p)[0] * sizeof(int));
                            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ahocorasick.c:356:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  int *nindex = (int*)malloc(INTEGER(wcount_p)[0] * sizeof(int));
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ahocorasick.c:362:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  int *ntext = (int*)malloc(INTEGER(wcount_p)[0] * sizeof(int));
                            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ahocorasick.c:368:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  int *strand = (int*)malloc(INTEGER(wcount_p)[0] * sizeof(int));
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ahocorasick.c:374:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  int *nmatch = (int*)malloc(INTEGER(wcount_p)[0] * sizeof(int));
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ahocorasick.c:432:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
          pos = getPos(get_complement(seq->seq.s[index]));
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ahocorasick.c:493:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
          pos = getPos(get_complement(seq->seq.s[index]));
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c collect.c -o collect.o
collect.c:23:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        ARRAY_RAW((*arr)) = malloc(sizeof(int)*size);
                                              ˜^˜˜˜
collect.c:42:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        ARRAY_RAW((*arr)) = malloc(sizeof(double)*size);
                                                 ˜^˜˜˜
collect.c:61:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        double* tmp = malloc(sizeof(double)*(arr->storage_len+size));
                                           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
collect.c:76:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        int* tmp = malloc(sizeof(int)*(arr->storage_len+size));
                                     ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c rm_small_peak.c -o rm_small_peak.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sort_by_genomic.c -o sort_by_genomic.o
sort_by_genomic.c:59:56: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        t_rec_ptr* recs = malloc(sizeof(t_rec_ptr)*start_arr->len);
                                                  ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
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 Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Starr.buildbin-libdir/Starr/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 (Starr)


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