Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch snpStats_1.10.0.tar.gz
StartedAt: 2013-05-01 11:07:24 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 11:11:03 -0700 (Wed, 01 May 2013)
EllapsedTime: 218.7 seconds
RetCode: 0
Status:  OK 
CheckDir: snpStats.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/snpStats.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'snpStats/DESCRIPTION' ... OK
* this is package 'snpStats' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'snpStats' can be installed ... [26s/28s] OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    2.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .Last.lib will not be used unless it is exported
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/snpStats.Rcheck/snpStats/libs/snpStats.so':
  Found non-API call to R: 'R_data_class'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [29s/30s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/snpStats.Rcheck/00check.log'
for details.

snpStats.Rcheck/00install.out:

* 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.Rcheck/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)

snpStats.Rcheck/snpStats-Ex.timings:

nameusersystemelapsed
Fst1.1440.1261.276
GlmEstimates-class0.0040.0060.010
GlmTests-class0.0070.0150.023
ImputationRules-class0.0040.0050.008
SingleSnpTests-class0.0050.0070.014
SnpMatrix-class0.3490.0900.441
XSnpMatrix-class0.1780.0410.221
chi.squared0.1390.0380.184
families0.0470.0150.063
filter.rules0.0020.0040.007
for.exercise2.1580.1482.325
ibsCount0.9180.0480.979
ibsDist0.4370.0180.460
imputation.maf0.0040.0060.010
impute.snps4.2460.2504.558
ld0.4320.0740.512
mean2g0.1480.0340.188
misinherits0.0940.0410.135
mvtests0.0030.0040.006
plotUncertainty0.0090.0140.024
pool0.2820.0430.327
pp0.1060.0230.133
qq.chisq0.0020.0040.007
read.beagle0.0030.0050.007
read.impute0.0030.0040.007
read.long0.0100.0110.021
read.mach0.0030.0050.007
read.pedfile0.0030.0050.009
row.summary0.2290.0400.275
single.snp.tests0.1640.0310.197
sm.compare0.0020.0030.006
snp.cor1.2060.0431.299
snp.imputation4.0520.2434.328
snp.lhs.estimates0.7200.1700.892
snp.lhs.tests0.1680.0420.217
snp.pre.multiply0.1870.0540.242
snp.rhs.estimates0.1930.0360.231
snp.rhs.tests0.1440.0380.183
switch.alleles0.1670.0550.222
tdt.snp0.0460.0300.081
test.allele.switch0.2820.0610.345
testdata0.2600.0530.315
write.plink0.3180.0300.350
xxt1.0810.0381.346