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Package 607/671HostnameOS / ArchBUILDCHECKBUILD BIN
snpStats 1.10.0
David Clayton
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/snpStats
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: snpStats
Version: 1.10.0
Command: rm -rf snpStats.buildbin-libdir && mkdir snpStats.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh snpStats_1.10.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R snpStats.buildbin-libdir
StartedAt: 2013-05-01 12:56:33 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:57:05 -0700 (Wed, 01 May 2013)
EllapsedTime: 32.2 seconds
RetCode: 0
Status:  OK 
PackageFile: snpStats_1.10.0.tgz
PackageFileSize: 7.024 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=snpStats.buildbin-libdir snpStats_1.10.0.tar.gz'
>>>>>>> 

* installing *source* package 'snpStats' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Runcertain.c -o Runcertain.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c adler32.c -o adler32.o
adler32.c:141:22: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
    rem = (unsigned)(len2 % BASE);
                     ^˜˜˜ ˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c bind.c -o bind.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c compress.c -o compress.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c count_gt.c -o count_gt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c covwin.c -o covwin.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c crc32.c -o crc32.o
crc32.c:275:47: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        c = crc_table[0][(c ^ *buf++) & 0xff] ^ (c >> 8);
          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
crc32.c:281:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:261:17: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                ^˜˜˜˜˜
crc32.c:260:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:281:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:261:25: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                        ^˜˜˜˜˜
crc32.c:260:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:281:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:261:33: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                ^˜˜˜˜˜
crc32.c:260:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:281:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:261:41: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                        ^˜˜˜˜˜
crc32.c:260:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:281:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:261:49: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                                ^˜˜˜˜˜
crc32.c:260:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:281:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:261:57: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                                        ^˜˜˜˜˜
crc32.c:260:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:281:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:261:65: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                                                ^˜˜˜˜˜
crc32.c:260:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:281:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:261:73: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                                                        ^˜˜˜˜˜
crc32.c:260:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:285:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT4;
        ^˜˜˜˜˜
crc32.c:260:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:291:47: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        c = crc_table[0][(c ^ *buf++) & 0xff] ^ (c >> 8);
          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
crc32.c:315:46: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        c = crc_table[4][(c >> 24) ^ *buf++] ^ (c << 8);
          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
crc32.c:322:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:301:17: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                ^˜˜˜˜˜
crc32.c:300:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:322:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:301:25: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                        ^˜˜˜˜˜
crc32.c:300:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:322:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:301:33: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                ^˜˜˜˜˜
crc32.c:300:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:322:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:301:41: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                        ^˜˜˜˜˜
crc32.c:300:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:322:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:301:49: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                                ^˜˜˜˜˜
crc32.c:300:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:322:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:301:57: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                                        ^˜˜˜˜˜
crc32.c:300:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:322:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:301:65: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                                                ^˜˜˜˜˜
crc32.c:300:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:322:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:301:73: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                                                        ^˜˜˜˜˜
crc32.c:300:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:326:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG4;
        ^˜˜˜˜˜
crc32.c:300:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:333:46: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        c = crc_table[4][(c >> 24) ^ *buf++] ^ (c << 8);
          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
22 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c deflate.c -o deflate.o
deflate.c:272:17: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
    s->w_bits = windowBits;
              ˜ ^˜˜˜˜˜˜˜˜˜
deflate.c:276:29: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
    s->hash_bits = memLevel + 7;
                 ˜ ˜˜˜˜˜˜˜˜˜^˜˜
deflate.c:462:21: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
    s->good_match = good_length;
                  ˜ ^˜˜˜˜˜˜˜˜˜˜
deflate.c:463:25: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
    s->max_lazy_match = max_lazy;
                      ˜ ^˜˜˜˜˜˜˜
deflate.c:465:27: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
    s->max_chain_length = max_chain;
                        ˜ ^˜˜˜˜˜˜˜˜
deflate.c:728:29: warning: implicit conversion loses integer precision: 'int' to 'Bytef' (aka 'unsigned char') [-Wconversion]
                put_byte(s, val);
                ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./deflate.h:275:57: note: expanded from macro 'put_byte'
#define put_byte(s, c) {s->pending_buf[s->pending++] = (c);}
                                                        ^
deflate.c:759:29: warning: implicit conversion loses integer precision: 'int' to 'Bytef' (aka 'unsigned char') [-Wconversion]
                put_byte(s, val);
                ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./deflate.h:275:57: note: expanded from macro 'put_byte'
#define put_byte(s, c) {s->pending_buf[s->pending++] = (c);}
                                                        ^
deflate.c:1071:23: warning: implicit conversion changes signedness: 'uInt' (aka 'unsigned int') to 'int' [-Wsign-conversion]
    int best_len = s->prev_length;              /* best match length so far */
        ˜˜˜˜˜˜˜˜   ˜˜˜^˜˜˜˜˜˜˜˜˜˜
deflate.c:1106:58: warning: implicit conversion changes signedness: 'uInt' (aka 'unsigned int') to 'int' [-Wsign-conversion]
    if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead;
                                                    ˜ ˜˜˜^˜˜˜˜˜˜˜˜
deflate.c:1380:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        n = read_buf(s->strm, s->window + s->strstart + s->lookahead, more);
          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
deflate.c:1495:24: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        max_start = s->block_start + max_block_size;
                    ˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
deflate.c:1564:44: warning: implicit conversion loses integer precision: 'unsigned int' to 'uch' (aka 'unsigned char') [-Wconversion]
                           s->match_length - MIN_MATCH, bflush);
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./deflate.h:327:16: note: expanded from macro '_tr_tally_dist'
  { uch len = (length); \
               ^
deflate.c:1563:43: warning: implicit conversion loses integer precision: 'unsigned int' to 'ush' (aka 'unsigned short') [-Wconversion]
            _tr_tally_dist(s, s->strstart - s->match_start,
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./deflate.h:328:17: note: expanded from macro '_tr_tally_dist'
    ush dist = (distance); \
                ^
deflate.c:1683:43: warning: implicit conversion loses integer precision: 'unsigned int' to 'uch' (aka 'unsigned char') [-Wconversion]
                           s->prev_length - MIN_MATCH, bflush);
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./deflate.h:327:16: note: expanded from macro '_tr_tally_dist'
  { uch len = (length); \
               ^
deflate.c:1682:46: warning: implicit conversion loses integer precision: 'unsigned int' to 'ush' (aka 'unsigned short') [-Wconversion]
            _tr_tally_dist(s, s->strstart -1 - s->prev_match,
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./deflate.h:328:17: note: expanded from macro '_tr_tally_dist'
    ush dist = (distance); \
                ^
deflate.c:1775:45: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
                s->match_length = MAX_MATCH - (int)(strend - scan);
                                ˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
deflate.c:1785:50: warning: implicit conversion loses integer precision: 'unsigned int' to 'uch' (aka 'unsigned char') [-Wconversion]
            _tr_tally_dist(s, 1, s->match_length - MIN_MATCH, bflush);
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./deflate.h:327:16: note: expanded from macro '_tr_tally_dist'
  { uch len = (length); \
               ^
17 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c force_hom.c -o force_hom.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c fst.c -o fst.o
fst.c:70:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(na, 0x00, ngrp*sizeof(int));
                   ^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
fst.c:70:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(na, 0x00, ngrp*sizeof(int));
                   ^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
fst.c:97:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(na, 0x00, ngrp*sizeof(int));
                     ^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
fst.c:97:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(na, 0x00, ngrp*sizeof(int));
                     ^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
fst.c:98:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(na2, 0x00, ngrp*sizeof(int));
                      ^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
fst.c:98:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(na2, 0x00, ngrp*sizeof(int));
                      ^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c glm_test.c -o glm_test.o
glm_test.c:424:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(U, 0x00, nc*P*sizeof(double));
                    ˜˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test.c:424:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(U, 0x00, nc*P*sizeof(double));
                    ˜˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test.c:478:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(Zri, 0x00, N*sizeof(double));
                        ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test.c:478:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(Zri, 0x00, N*sizeof(double));
                        ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test.c:596:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(Uc, 0x00, C*P*sizeof(double));
                     ˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test.c:596:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(Uc, 0x00, C*P*sizeof(double));
                     ˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test.c:614:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(meatrix,  0x00, sizeof(double)*(P*(P+1))/2);
                                         ˜ ˜^˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test.c:614:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(meatrix,  0x00, sizeof(double)*(P*(P+1))/2);
                                         ˜ ˜^˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c glm_test_R.c -o glm_test_R.o
glm_test_R.c:59:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sstype = TYPEOF(Snp_subset);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:173:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *yd = (double *) R_alloc(N, sizeof(double));
                          ˜˜˜˜˜˜˜ ^
glm_test_R.c:174:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *fitted = (double *) R_alloc(N, sizeof(double));
                              ˜˜˜˜˜˜˜ ^
glm_test_R.c:175:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *prior = (double *) R_alloc(N, sizeof(double));
                             ˜˜˜˜˜˜˜ ^
glm_test_R.c:176:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *resid = (double *) R_alloc(N, sizeof(double));
                             ˜˜˜˜˜˜˜ ^
glm_test_R.c:177:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *weights = (double *) R_alloc(N, sizeof(double));
                               ˜˜˜˜˜˜˜ ^
glm_test_R.c:180:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    xb = (double *) R_alloc(N*M, sizeof(double));
                    ˜˜˜˜˜˜˜ ˜^˜
glm_test_R.c:191:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sntype = TYPEOF(snpNames);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:256:17: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
        yd[i] = g2mean(yij)/2.0;
                ˜˜˜˜˜˜ ^˜˜
glm_test_R.c:267:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(u, 0x00, P*sizeof(double));
                      ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test_R.c:267:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(u, 0x00, P*sizeof(double));
                      ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test_R.c:268:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(v, 0x00, sizeof(double)*(P*(P+1))/2); 
                                    ˜ ˜^˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test_R.c:268:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(v, 0x00, sizeof(double)*(P*(P+1))/2); 
                                    ˜ ˜^˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test_R.c:296:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(u, 0x00, P*sizeof(double));
                        ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test_R.c:296:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(u, 0x00, P*sizeof(double));
                        ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test_R.c:297:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(v, 0x00, sizeof(double)*(P*(P+1))/2);
                                      ˜ ˜^˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test_R.c:297:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(v, 0x00, sizeof(double)*(P*(P+1))/2);
                                      ˜ ˜^˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test_R.c:513:25: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE tests_type = TYPEOF(Tests);
           ˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:582:20: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int mallowed = N * REAL(MissAllow)[0];
      ˜˜˜˜˜˜˜˜   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:591:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *zw = (double *) R_alloc(N*test_size, sizeof(double));
                          ˜˜˜˜˜˜˜ ˜^˜˜˜˜˜˜˜˜˜
glm_test_R.c:592:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *prior = (double *) R_alloc(N, sizeof(double));
                             ˜˜˜˜˜˜˜ ^
glm_test_R.c:593:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *resid = (double *) R_alloc(N, sizeof(double));
                             ˜˜˜˜˜˜˜ ^
glm_test_R.c:594:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *resid_all = (double *) R_alloc(N, sizeof(double));
                                 ˜˜˜˜˜˜˜ ^
glm_test_R.c:595:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *weights = (double *) R_alloc(N, sizeof(double));
                               ˜˜˜˜˜˜˜ ^
glm_test_R.c:596:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *weights_all = (double *) R_alloc(N, sizeof(double));
                                   ˜˜˜˜˜˜˜ ^
glm_test_R.c:597:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *fitted = (double *) R_alloc(N, sizeof(double));
                              ˜˜˜˜˜˜˜ ^
glm_test_R.c:598:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *fitted_all = (double *) R_alloc(N, sizeof(double));
                                  ˜˜˜˜˜˜˜ ^
glm_test_R.c:601:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    xb = (double *) R_alloc(N*M, sizeof(double));
                    ˜˜˜˜˜˜˜ ˜^˜
glm_test_R.c:602:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    xb_all = (double *) R_alloc(N*M, sizeof(double));
                        ˜˜˜˜˜˜˜ ˜^˜
glm_test_R.c:761:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(u, 0x00, nsnpt*sizeof(double));
                      ^˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test_R.c:761:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(u, 0x00, nsnpt*sizeof(double));
                      ^˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test_R.c:762:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(v, 0x00, sizeof(double)*(nsnpt*(nsnpt+1))/2);
                                    ˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test_R.c:762:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(v, 0x00, sizeof(double)*(nsnpt*(nsnpt+1))/2);
                                    ˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test_R.c:929:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(ru, 0x00, nu*sizeof(double));
                     ^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test_R.c:929:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(ru, 0x00, nu*sizeof(double));
                     ^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test_R.c:930:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(rv, 0x00, nv*sizeof(double));
                     ^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
glm_test_R.c:930:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(rv, 0x00, nv*sizeof(double));
                     ^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
glm_test_R.c:1043:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sstype = TYPEOF(Snp_subset);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:1144:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *yd = (double *) R_alloc(N, sizeof(double));
                          ˜˜˜˜˜˜˜ ^
glm_test_R.c:1145:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *fitted = (double *) R_alloc(N, sizeof(double));
                              ˜˜˜˜˜˜˜ ^
glm_test_R.c:1146:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *prior = (double *) R_alloc(N, sizeof(double));
                             ˜˜˜˜˜˜˜ ^
glm_test_R.c:1147:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *resid = (double *) R_alloc(N, sizeof(double));
                             ˜˜˜˜˜˜˜ ^
glm_test_R.c:1148:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *weights = (double *) R_alloc(N, sizeof(double));
                               ˜˜˜˜˜˜˜ ^
glm_test_R.c:1149:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *xb = (double *) R_alloc(N*M, sizeof(double));
                          ˜˜˜˜˜˜˜ ˜^˜
glm_test_R.c:1151:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  int *which = (int *) R_alloc(P, sizeof(int));
                       ˜˜˜˜˜˜˜ ^
glm_test_R.c:1152:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *beta = (double *) R_alloc(P, sizeof(double));
                            ˜˜˜˜˜˜˜ ^
glm_test_R.c:1153:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *tri = (double *) R_alloc((P*(P+1))/2, sizeof(double));
                           ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
glm_test_R.c:1161:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sntype = TYPEOF(snpNames);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:1205:17: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
        yd[i] = g2mean(yij)/2.0;
                ˜˜˜˜˜˜ ^˜˜
glm_test_R.c:1441:24: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sets_type = TYPEOF(Sets);
           ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:1510:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *new_prior = (double *) R_alloc(N, sizeof(double));
                                 ˜˜˜˜˜˜˜ ^
glm_test_R.c:1511:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *resid = (double *) R_alloc(N, sizeof(double));
                             ˜˜˜˜˜˜˜ ^
glm_test_R.c:1512:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *weights = (double *) R_alloc(N, sizeof(double));
                               ˜˜˜˜˜˜˜ ^
glm_test_R.c:1513:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *fitted = (double *) R_alloc(N, sizeof(double));
                              ˜˜˜˜˜˜˜ ^
glm_test_R.c:1514:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *xb = (double *) R_alloc(N*M_max, sizeof(double));
                          ˜˜˜˜˜˜˜ ˜^˜˜˜˜˜
glm_test_R.c:1515:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *xz = (double *) R_alloc(N*M_max, sizeof(double));
                          ˜˜˜˜˜˜˜ ˜^˜˜˜˜˜
glm_test_R.c:1517:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *beta =  (double *) R_alloc(M_max, sizeof(double));
                             ˜˜˜˜˜˜˜ ^˜˜˜˜
glm_test_R.c:1518:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  int *which = (int *) R_alloc(M_max, sizeof(int));
                       ˜˜˜˜˜˜˜ ^˜˜˜˜
glm_test_R.c:1519:53: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  double *tri = (double *) R_alloc((M_max*(M_max+1))/2, sizeof(double));
                           ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
glm_test_R.c:1523:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    Uc = (double *) R_alloc(C*M_max, sizeof(double));
                    ˜˜˜˜˜˜˜ ˜^˜˜˜˜˜
glm_test_R.c:1623:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
          int len = strlen(setname);
              ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
61 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c gzclose.c -o gzclose.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c gzlib.c -o gzlib.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c gzread.c -o gzread.o
gzread.c:34:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        *have += ret;
              ˜˜ ^˜˜
gzread.c:31:15: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        ret = read(state->fd, buf + *have, len - *have);
            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gzread.c:81:11: warning: operand of ? changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    val = NEXT();
        ˜ ^˜˜˜˜˜
gzread.c:67:66: note: expanded from macro 'NEXT'
#define NEXT() ((strm->avail_in == 0 && gz_avail(state) == -1) ? -1 : \
                                                                 ^˜
gzread.c:81:11: warning: operand of ? changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    val = NEXT();
        ˜ ^˜˜˜˜˜
gzread.c:68:40: note: expanded from macro 'NEXT'
                (strm->avail_in == 0 ? -1 : \
                                       ^˜
gzread.c:190:17: warning: expression result unused [-Wunused-value]
                NEXT();
                ^˜˜˜˜˜
gzread.c:67:66: note: expanded from macro 'NEXT'
#define NEXT() ((strm->avail_in == 0 && gz_avail(state) == -1) ? -1 : \
                                                                 ^˜
gzread.c:191:17: warning: expression result unused [-Wunused-value]
                NEXT();
                ^˜˜˜˜˜
gzread.c:67:66: note: expanded from macro 'NEXT'
#define NEXT() ((strm->avail_in == 0 && gz_avail(state) == -1) ? -1 : \
                                                                 ^˜
gzread.c:170:13: warning: expression result unused [-Wunused-value]
            NEXT();                 /* modification time */
            ^˜˜˜˜˜
gzread.c:67:66: note: expanded from macro 'NEXT'
#define NEXT() ((strm->avail_in == 0 && gz_avail(state) == -1) ? -1 : \
                                                                 ^˜
gzread.c:171:13: warning: expression result unused [-Wunused-value]
            NEXT();
            ^˜˜˜˜˜
gzread.c:67:66: note: expanded from macro 'NEXT'
#define NEXT() ((strm->avail_in == 0 && gz_avail(state) == -1) ? -1 : \
                                                                 ^˜
gzread.c:172:13: warning: expression result unused [-Wunused-value]
            NEXT();
            ^˜˜˜˜˜
gzread.c:67:66: note: expanded from macro 'NEXT'
#define NEXT() ((strm->avail_in == 0 && gz_avail(state) == -1) ? -1 : \
                                                                 ^˜
gzread.c:173:13: warning: expression result unused [-Wunused-value]
            NEXT();
            ^˜˜˜˜˜
gzread.c:67:66: note: expanded from macro 'NEXT'
#define NEXT() ((strm->avail_in == 0 && gz_avail(state) == -1) ? -1 : \
                                                                 ^˜
gzread.c:174:13: warning: expression result unused [-Wunused-value]
            NEXT();                 /* extra flags */
            ^˜˜˜˜˜
gzread.c:67:66: note: expanded from macro 'NEXT'
#define NEXT() ((strm->avail_in == 0 && gz_avail(state) == -1) ? -1 : \
                                                                 ^˜
gzread.c:175:13: warning: expression result unused [-Wunused-value]
            NEXT();                 /* operating system */
            ^˜˜˜˜˜
gzread.c:67:66: note: expanded from macro 'NEXT'
#define NEXT() ((strm->avail_in == 0 && gz_avail(state) == -1) ? -1 : \
                                                                 ^˜
gzread.c:512:26: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
        state->next[0] = c;
                       ˜ ^
gzread.c:533:22: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
    state->next[0] = c;
                   ˜ ^
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c gzwrite.c -o gzwrite.o
gzwrite.c:79:33: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
            if (have && ((got = write(state->fd, state->next, have)) < 0 ||
                              ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gzwrite.c:251:43: warning: implicit conversion loses integer precision: 'int' to 'Bytef' (aka 'unsigned char') [-Wconversion]
        strm->next_in[strm->avail_in++] = c;
                                        ˜ ^
gzwrite.c:257:14: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
    buf[0] = c;
           ˜ ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c hash_index.c -o hash_index.o
hash_index.c:58:10: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
    h += *s;
      ˜˜ ^˜
hash_index.c:60:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  return (h & bitmask);
            ˜ ^˜˜˜˜˜˜
hash_index.c:69:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    result->nodelist =(t_node *)calloc(hash_size, sizeof(t_node));
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
hash_index.c:82:17: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      int idx = hash(name, db->bitmask);
          ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
hash_index.c:108:27: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
    *dup_low = (*dup_low) & 0xDF;
             ˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c hphase.c -o hphase.o
hphase.c:20:25: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
  memset(alleles, 0x00, nsnp*sizeof(int));
                        ^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
hphase.c:20:25: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
  memset(alleles, 0x00, nsnp*sizeof(int));
                        ^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
hphase.c:204:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(sum, 0x00, nht*sizeof(double));
                      ^˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
hphase.c:204:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(sum, 0x00, nht*sizeof(double));
                      ^˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imputation.c -o imputation.o
imputation.c:61:18: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int maxit_em = REAL(EMcontr)[0];  /* Max EM iterations */
      ˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
imputation.c:63:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int maxit_ipf = REAL(EMcontr)[2]; /* Max iterations for initial IPF */
      ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
imputation.c:64:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int tol_ipf = REAL(EMcontr)[3]; /* Convergence tolerance for initial IPF */
      ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
imputation.c:250:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
              tcell[j] = tcell[j] | (xkj << sh);
                       ˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
imputation.c:250:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
              tcell[j] = tcell[j] | (xkj << sh);
                         ^˜˜˜˜˜˜˜ ˜
imputation.c:255:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          memset(contin, 0x00, tsize*sizeof(int));
                               ^˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
imputation.c:255:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          memset(contin, 0x00, tsize*sizeof(int));
                               ^˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
imputation.c:257:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memset(hcontin, 0x00, tsize*sizeof(int));
                                  ^˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
imputation.c:257:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memset(hcontin, 0x00, tsize*sizeof(int));
                                  ^˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
imputation.c:654:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(gt, 0x00, nuse*sizeof(int));
                     ^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
imputation.c:654:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(gt, 0x00, nuse*sizeof(int));
                     ^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
imputation.c:715:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sutype = TYPEOF(Subset);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c in.c -o in.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c infback.c -o infback.o
infback.c:55:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    state->wbits = windowBits;
                 ˜ ^˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c inffast.c -o inffast.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c inflate.c -o inflate.o
inflate.c:223:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    if (bits > 16 || state->bits + bits > 32) return Z_STREAM_ERROR;
                                 ˜ ^˜˜˜
inflate.c:225:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    state->hold += value << state->bits;
                ˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
inflate.c:226:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    state->bits += bits;
                ˜˜ ^˜˜˜
inflate.c:748:62: warning: implicit conversion loses integer precision: 'unsigned int' to 'Bytef' (aka 'unsigned char') [-Wconversion]
                        state->head->name[state->length++] = len;
                                                           ˜ ^˜˜
inflate.c:769:65: warning: implicit conversion loses integer precision: 'unsigned int' to 'Bytef' (aka 'unsigned char') [-Wconversion]
                        state->head->comment[state->length++] = len;
                                                              ˜ ^˜˜
inflate.c:1231:55: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                      (state->mode == TYPE ? 128 : 0) +
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c inftrees.c -o inftrees.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c input.c -o input.o
input.c:362:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      int lfn = strlen(filename); 
          ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input.c:733:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int la = strlen(a), lb = strlen(b);
        ˜˜   ^˜˜˜˜˜˜˜˜
input.c:733:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int la = strlen(a), lb = strlen(b);
                        ˜˜   ^˜˜˜˜˜˜˜˜
input.c:761:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
  char cu = toupper(c);
       ˜˜   ^˜˜˜˜˜˜˜˜˜
input.c:786:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    lenf = lenb = strlen(front);
                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
input.c:807:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int lenx = strlen(xi);
        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜
input.c:959:28: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
      memset(matrix, 0x00, N*sizeof(unsigned char));
                           ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
input.c:959:28: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
      memset(matrix, 0x00, N*sizeof(unsigned char));
                           ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c invert.c -o invert.o
invert.c:136:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    W = (double *) calloc((N*(N+1))/2, sizeof(double));
                   ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ipf.c -o ipf.o
ipf.c:84:25: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
      int mbytes = msize*sizeof(double);
          ˜˜˜˜˜˜   ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ipf.c:84:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      int mbytes = msize*sizeof(double);
                   ^˜˜˜˜˜
ipf.c:89:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int mi = bitxtr(i, mask);
            ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ipf.c:106:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int mi = bitxtr(i, mask);
            ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ld.c -o ld.o
ld.c:349:10: warning: unused variable 'OR' [-Wunused-variable]
  double OR =  ad/bc;
         ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c misc.c -o misc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mla.c -o mla.o
mla.c:32:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(swy, 0x00, nstrata*sizeof(double));
                      ^˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mla.c:32:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(swy, 0x00, nstrata*sizeof(double));
                      ^˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mla.c:33:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(swt, 0x00, nstrata*sizeof(double));
                      ^˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mla.c:33:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(swt, 0x00, nstrata*sizeof(double));
                      ^˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mvphenotype.c -o mvphenotype.o
mvphenotype.c:26:22: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
  memset(sumx, 0x00, Mx*sizeof(double));
                     ^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mvphenotype.c:26:22: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
  memset(sumx, 0x00, Mx*sizeof(double));
                     ^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mvphenotype.c:31:24: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
    memset(sumy, 0x00, My*sizeof(double));
                       ^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mvphenotype.c:31:24: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
    memset(sumy, 0x00, My*sizeof(double));
                       ^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mvphenotype.c:37:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(ssp, 0x00, nssp*sizeof(double));
                    ^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mvphenotype.c:37:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(ssp, 0x00, nssp*sizeof(double));
                    ^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mvphenotype.c:61:26: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
      memset(sumx, 0x00, Mx*sizeof(double));
                         ^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mvphenotype.c:61:26: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
      memset(sumx, 0x00, Mx*sizeof(double));
                         ^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mvphenotype.c:63:21: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
        memset(sumy, 0x00, My*sizeof(double));
                           ^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mvphenotype.c:63:21: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
        memset(sumy, 0x00, My*sizeof(double));
                           ^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mvphenotype.c:226:25: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE tests_type = TYPEOF(Tests);
           ˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
mvphenotype.c:342:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(xmiss, 0x00, N*sizeof(int));
                      ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mvphenotype.c:342:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(xmiss, 0x00, N*sizeof(int));
                      ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mvphenotype.c:400:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(lorder_t, 0x00, N*sizeof(int));
                             ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mvphenotype.c:400:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(lorder_t, 0x00, N*sizeof(int));
                             ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mvphenotype.c:408:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(xmiss, 0x00, N*sizeof(int));
                        ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mvphenotype.c:408:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(xmiss, 0x00, N*sizeof(int));
                        ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mvphenotype.c:567:7: warning: variable 'df_rV' is uninitialized when used here [-Wuninitialized]
        Free(df_rV);
             ^˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:64:46: note: expanded from macro 'Free'
#define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
                                             ^
mvphenotype.c:485:20: note: initialize the variable 'df_rV' to silence this warning
      double *df_rV; 
                   ^
                    = NULL
18 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c outdata.c -o outdata.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c plink.c -o plink.o
plink.c:161:14: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
        byte = byte | (recode[s] << 2*part);
             ˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
plink.c:180:14: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
        byte = byte | (recode[s]<<2*part);
             ˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c read_uncertain.c -o read_uncertain.o
read_uncertain.c:38:21: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
  while (isspace(ch=gzgetc(infile))){} /* Skip leading white space */
                   ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
read_uncertain.c:45:25: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
  } while (!(isspace(ch=gzgetc(infile))));
                       ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
read_uncertain.c:53:18: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE tns = TYPEOF(Nsubject);
           ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
read_uncertain.c:75:24: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    ncol = words/lines - 2;
         ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
read_uncertain.c:80:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    ncol = words -2;
         ˜ ˜˜˜˜˜˜^˜
read_uncertain.c:99:40: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  PROTECT(Result = allocMatrix(RAWSXP, lines, ncol));
                   ˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
read_uncertain.c:170:18: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE tns = TYPEOF(Nsnp);
           ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
read_uncertain.c:181:9: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  tns = TYPEOF(Snpcol);
      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
read_uncertain.c:211:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    N = words/lines - ncol_skip;
      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
read_uncertain.c:212:12: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    nsnp = lines;
         ˜ ^˜˜˜˜
read_uncertain.c:216:15: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    N = words - ncol_skip;
      ˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c readped.c -o readped.o
readped.c:96:17: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
    acodes[0] = a1;
              ˜ ^˜
readped.c:100:19: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
      acodes[1] = a2;
                ˜ ^˜
readped.c:109:14: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
        acodes[1] = a2;
                  ˜ ^˜
readped.c:114:19: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
      acodes[1] = a1;
                ˜ ^˜
readped.c:118:19: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
      acodes[1] = a1;
                ˜ ^˜
readped.c:193:17: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
    acodes[i] = mval;
              ˜ ^˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c single_snp_tests.c -o single_snp_tests.o
single_snp_tests.c:38:20: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE stype = TYPEOF(Stratum);
           ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
single_snp_tests.c:94:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sutype = TYPEOF(Subset);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜
single_snp_tests.c:123:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sstype = TYPEOF(Snp_subset);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c snp_summary.c -o snp_summary.o
snp_summary.c:204:13: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
            g2post(g, &p0, &p1, &p2);
            ˜˜˜˜˜˜ ^
snp_summary.c:232:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    calls_diploid[j] = nv;
                     ˜ ^˜
snp_summary.c:455:13: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
            g2post(g, &p0, &p1, &p2);
            ˜˜˜˜˜˜ ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c snpmpy.c -o snpmpy.o
snpmpy.c:93:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, P*M*sizeof(double));
                       ˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
snpmpy.c:93:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, P*M*sizeof(double));
                       ˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
snpmpy.c:108:20: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
        unsigned char w = (int) snps[ki++];
                      ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
snpmpy.c:135:24: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
          double xik = g2mean(sik) - mean;
                       ˜˜˜˜˜˜ ^˜˜
snpmpy.c:216:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, N*P*sizeof(double));
                       ˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
snpmpy.c:216:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, N*P*sizeof(double));
                       ˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
snpmpy.c:231:20: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
        unsigned char w = (int) snps[ki++];
                      ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
snpmpy.c:258:24: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
          double xik = g2mean(sik) - mean;
                       ˜˜˜˜˜˜ ^˜˜
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c solve_cubic.c -o solve_cubic.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c structure.c -o structure.o
structure.c:117:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(Ti, 0x00, N*sizeof(int));
                     ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
structure.c:117:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(Ti, 0x00, N*sizeof(int));
                     ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
structure.c:119:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(Tk, 0x00, M*sizeof(int));
                     ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
structure.c:119:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(Tk, 0x00, M*sizeof(int));
                     ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
structure.c:149:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, N*N*sizeof(double));
                       ˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
structure.c:149:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, N*N*sizeof(double));
                       ˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
structure.c:161:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(count, 0x00, nstrata*sizeof(int));
                          ^˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
structure.c:161:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(count, 0x00, nstrata*sizeof(int));
                          ^˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
structure.c:162:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(acount, 0x00, nstrata*sizeof(double));
                           ^˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
structure.c:162:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(acount, 0x00, nstrata*sizeof(double));
                           ^˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
structure.c:441:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, N*N*sizeof(double));
                       ˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
structure.c:441:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, N*N*sizeof(double));
                       ˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
structure.c:531:24: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, Nout*sizeof(double));
                       ^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
structure.c:531:24: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, Nout*sizeof(double));
                       ^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c switch.c -o switch.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c tdt.c -o tdt.o
tdt.c:103:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sstype = TYPEOF(Snp_subset);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c trees.c -o trees.o
trees.c:531:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        s->opt_len += (ulg)f * (bits + xbits);
                             ˜  ˜˜˜˜˜^˜˜˜˜˜˜
trees.c:532:60: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        if (stree) s->static_len += (ulg)f * (stree[n].Len + xbits);
                                           ˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
trees.c:565:31: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
                              *(long)tree[m].Freq;
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:595:60: warning: implicit conversion loses integer precision: 'int' to 'ush' (aka 'unsigned short') [-Wconversion]
        next_code[bits] = code = (code + bl_count[bits-1]) << 1;
                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
trees.c:608:24: warning: implicit conversion loses integer precision: 'unsigned int' to 'ush' (aka 'unsigned short') [-Wconversion]
        tree[n].Code = bi_reverse(next_code[len]++, len);
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:777:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            do { send_code(s, curlen, s->bl_tree); } while (--count != 0);
                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:777:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            do { send_code(s, curlen, s->bl_tree); } while (--count != 0);
                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:781:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_code(s, curlen, s->bl_tree); count--;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:781:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_code(s, curlen, s->bl_tree); count--;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:784:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REP_3_6, s->bl_tree); send_bits(s, count-3, 2);
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:784:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REP_3_6, s->bl_tree); send_bits(s, count-3, 2);
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:784:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REP_3_6, s->bl_tree); send_bits(s, count-3, 2);
                                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:784:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REP_3_6, s->bl_tree); send_bits(s, count-3, 2);
                                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:787:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REPZ_3_10, s->bl_tree); send_bits(s, count-3, 3);
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:787:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REPZ_3_10, s->bl_tree); send_bits(s, count-3, 3);
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:787:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REPZ_3_10, s->bl_tree); send_bits(s, count-3, 3);
                                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:787:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REPZ_3_10, s->bl_tree); send_bits(s, count-3, 3);
                                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:790:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REPZ_11_138, s->bl_tree); send_bits(s, count-11, 7);
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:790:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REPZ_11_138, s->bl_tree); send_bits(s, count-11, 7);
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:790:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REPZ_11_138, s->bl_tree); send_bits(s, count-11, 7);
                                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:790:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, REPZ_11_138, s->bl_tree); send_bits(s, count-11, 7);
                                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:830:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    s->opt_len += 3*(max_blindex+1) + 5+5+4;
               ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
trees.c:852:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, lcodes-257, 5); /* not +255 as stated in appnote.txt */
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:852:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, lcodes-257, 5); /* not +255 as stated in appnote.txt */
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:853:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, dcodes-1,   5);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:853:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, dcodes-1,   5);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:854:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, blcodes-4,  4); /* not -3 as stated in appnote.txt */
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:854:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, blcodes-4,  4); /* not -3 as stated in appnote.txt */
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:857:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, s->bl_tree[bl_order[rank]].Len, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:857:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, s->bl_tree[bl_order[rank]].Len, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:877:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, (STORED_BLOCK<<1)+last, 3);    /* send block type */
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:877:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, (STORED_BLOCK<<1)+last, 3);    /* send block type */
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:899:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, STATIC_TREES<<1, 3);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:899:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, STATIC_TREES<<1, 3);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:900:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_code(s, END_BLOCK, static_ltree);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:900:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_code(s, END_BLOCK, static_ltree);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:911:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, STATIC_TREES<<1, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:911:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, STATIC_TREES<<1, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:912:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_code(s, END_BLOCK, static_ltree);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:912:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_code(s, END_BLOCK, static_ltree);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:992:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, (STATIC_TREES<<1)+last, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:992:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, (STATIC_TREES<<1)+last, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:998:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, (DYN_TREES<<1)+last, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:998:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, (DYN_TREES<<1)+last, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1091:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, lc, ltree); /* send a literal byte */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1091:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, lc, ltree); /* send a literal byte */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1096:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, code+LITERALS+1, ltree); /* send the length code */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1096:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, code+LITERALS+1, ltree); /* send the length code */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1100:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_bits(s, lc, extra);       /* send the extra length bits */
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1100:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_bits(s, lc, extra);       /* send the extra length bits */
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1106:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, code, dtree);       /* send the distance code */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1106:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, code, dtree);       /* send the distance code */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1109:25: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
                dist -= base_dist[code];
                     ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:1110:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                send_bits(s, dist, extra);   /* send the extra distance bits */
                ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
trees.c:221:15: note: expanded from macro 'send_bits'
    int val = value;\
              ^
trees.c:1110:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_bits(s, dist, extra);   /* send the extra distance bits */
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1110:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_bits(s, dist, extra);   /* send the extra distance bits */
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1120:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_code(s, END_BLOCK, ltree);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1120:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_code(s, END_BLOCK, ltree);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:168:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:225:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1242:21: warning: implicit conversion changes signedness: 'charf' (aka 'char') to 'Bytef' (aka 'unsigned char') [-Wsign-conversion]
        put_byte(s, *buf++);
        ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./deflate.h:275:57: note: expanded from macro 'put_byte'
#define put_byte(s, c) {s->pending_buf[s->pending++] = (c);}
                                                        ^
59 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c uncertain.c -o uncertain.o
uncertain.c:116:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int iAA = floor(pAA+0.499999);
      ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
uncertain.c:117:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int iAB = floor(pAB+0.499999);
      ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
uncertain.c:118:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int iBB = floor(pBB+0.499999);
      ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c uncompr.c -o uncompr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c zutil.c -o zutil.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o snpStats.so Runcertain.o adler32.o bind.o compress.o count_gt.o covwin.o crc32.o deflate.o force_hom.o fst.o glm_test.o glm_test_R.o gzclose.o gzlib.o gzread.o gzwrite.o hash_index.o hphase.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o invert.o ipf.o ld.o misc.o mla.o mvphenotype.o outdata.o plink.o read_uncertain.o readped.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o structure.o switch.o tdt.o trees.o uncertain.o uncompr.o zutil.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/snpStats.buildbin-libdir/snpStats/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'snpStats'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (snpStats)


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