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Package 121/671HostnameOS / ArchBUILDCHECKBUILD BIN
chopsticks 1.24.1
Hin-Tak Leung
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/chopsticks
Last Changed Rev: 75627 / Revision: 76155
Last Changed Date: 2013-04-13 12:10:48 -0700 (Sat, 13 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: chopsticks
Version: 1.24.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chopsticks_1.24.1.tar.gz
StartedAt: 2013-05-01 03:46:56 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 03:48:10 -0700 (Wed, 01 May 2013)
EllapsedTime: 74.0 seconds
RetCode: 0
Status:  OK 
CheckDir: chopsticks.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/chopsticks.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 'chopsticks/DESCRIPTION' ... OK
* this is package 'chopsticks' version '1.24.1'
* 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 'chopsticks' can be installed ... [8s/10s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    1.1Mb
* 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
File 'chopsticks/R/zzz.R':
  .Last.lib has wrong argument list 'libname, package'

Package detach functions should have one arguments with names starting
  with 'lib'.
Package detach functions should not call 'library.dynam.unload'.
See section 'Good practice' in '?.Last.lib'.
* checking Rd files ... NOTE
prepare_Rd: ibs.stats.Rd:28: Dropping empty section \references
prepare_Rd: ibs.stats.Rd:49: Dropping empty section \seealso
prepare_Rd: read.pedfile.info.Rd:31-32: Dropping empty section \examples
prepare_Rd: read.pedfile.map.Rd:31-32: Dropping empty section \examples
prepare_Rd: read.snps.chiamo.Rd:37-38: Dropping empty section \note
prepare_Rd: read.wtccc.signals.Rd:58: Dropping empty section \seealso
prepare_Rd: wtccc.sample.list.Rd:36-37: Dropping empty section \note
prepare_Rd: wtccc.sample.list.Rd:39-40: Dropping empty section \examples
* 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/chopsticks.Rcheck/chopsticks/libs/chopsticks.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 ... [13s/13s] 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 4 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/chopsticks.Rcheck/00check.log'
for details.

chopsticks.Rcheck/00install.out:

* installing *source* package 'chopsticks' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c adler32.c -o adler32.o
adler32.c:138:22: warning: implicit conversion changes signedness: 'long' to 'unsigned 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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -Wall -pedantic -Wconversion -c crc32.c -o crc32.o
crc32.c:273:47: 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:279:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:259:17: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                ^˜˜˜˜˜
crc32.c:258:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:279:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:259:25: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                        ^˜˜˜˜˜
crc32.c:258:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:279:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:259:33: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                ^˜˜˜˜˜
crc32.c:258:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:279:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:259:41: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                        ^˜˜˜˜˜
crc32.c:258:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:279:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:259:49: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                                ^˜˜˜˜˜
crc32.c:258:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:279:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:259:57: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                                        ^˜˜˜˜˜
crc32.c:258:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:279:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:259:65: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                                                ^˜˜˜˜˜
crc32.c:258:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:279:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT32;
        ^˜˜˜˜˜˜
crc32.c:259:73: note: expanded from macro 'DOLIT32'
#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
                                                                        ^˜˜˜˜˜
crc32.c:258:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:283:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOLIT4;
        ^˜˜˜˜˜
crc32.c:258:44: note: expanded from macro 'DOLIT4'
            crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:289:47: 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:313:46: 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:320:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:299:17: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                ^˜˜˜˜˜
crc32.c:298:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:320:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:299:25: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                        ^˜˜˜˜˜
crc32.c:298:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:320:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:299:33: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                ^˜˜˜˜˜
crc32.c:298:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:320:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:299:41: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                        ^˜˜˜˜˜
crc32.c:298:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:320:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:299:49: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                                ^˜˜˜˜˜
crc32.c:298:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:320:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:299:57: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                                        ^˜˜˜˜˜
crc32.c:298:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:320:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:299:65: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                                                ^˜˜˜˜˜
crc32.c:298:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:320:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG32;
        ^˜˜˜˜˜˜
crc32.c:299:73: note: expanded from macro 'DOBIG32'
#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
                                                                        ^˜˜˜˜˜
crc32.c:298:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:324:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'u4' (aka 'unsigned int') [-Wshorten-64-to-32]
        DOBIG4;
        ^˜˜˜˜˜
crc32.c:298:44: note: expanded from macro 'DOBIG4'
            crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
crc32.c:331:46: 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 -ggdb -O0 -Wall -pedantic -Wconversion -c deflate.c -o deflate.o
deflate.c:278:17: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
    s->w_bits = windowBits;
              ˜ ^˜˜˜˜˜˜˜˜˜
deflate.c:282:29: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
    s->hash_bits = memLevel + 7;
                 ˜ ˜˜˜˜˜˜˜˜˜^˜˜
deflate.c:465:21: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
    s->good_match = good_length;
                  ˜ ^˜˜˜˜˜˜˜˜˜˜
deflate.c:466:25: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
    s->max_lazy_match = max_lazy;
                      ˜ ^˜˜˜˜˜˜˜
deflate.c:468:27: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
    s->max_chain_length = max_chain;
                        ˜ ^˜˜˜˜˜˜˜˜
deflate.c:698:29: warning: implicit conversion loses integer precision: 'int' to 'Bytef' (aka 'unsigned char') [-Wconversion]
                put_byte(s, val);
                ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./deflate.h:268:57: note: expanded from macro 'put_byte'
#define put_byte(s, c) {s->pending_buf[s->pending++] = (c);}
                                                        ^
deflate.c:729:29: warning: implicit conversion loses integer precision: 'int' to 'Bytef' (aka 'unsigned char') [-Wconversion]
                put_byte(s, val);
                ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./deflate.h:268:57: note: expanded from macro 'put_byte'
#define put_byte(s, c) {s->pending_buf[s->pending++] = (c);}
                                                        ^
deflate.c:1035:23: 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:1070:58: 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:1342:13: 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:1423:24: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        max_start = s->block_start + max_block_size;
                    ˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
deflate.c:1502:44: warning: implicit conversion loses integer precision: 'unsigned int' to 'uch' (aka 'unsigned char') [-Wconversion]
                           s->match_length - MIN_MATCH, bflush);
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./deflate.h:316:16: note: expanded from macro '_tr_tally_dist'
  { uch len = (length); \
               ^
deflate.c:1501:43: 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:317:17: note: expanded from macro '_tr_tally_dist'
    ush dist = (distance); \
                ^
deflate.c:1624:43: warning: implicit conversion loses integer precision: 'unsigned int' to 'uch' (aka 'unsigned char') [-Wconversion]
                           s->prev_length - MIN_MATCH, bflush);
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./deflate.h:316:16: note: expanded from macro '_tr_tally_dist'
  { uch len = (length); \
               ^
deflate.c:1623:46: 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:317:17: note: expanded from macro '_tr_tally_dist'
    ush dist = (distance); \
                ^
15 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -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 -ggdb -O0 -Wall -pedantic -Wconversion -c glm_test.c -o glm_test.o
glm_test.c:107:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      double *yw = (double *) calloc(N, sizeof(double));
                              ˜˜˜˜˜˜ ^
glm_test.c:155:21: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
          (iter && (abs(wss-wss_last)/wss_last < conv));
                    ˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜
glm_test.c:331:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  Zri = Zr = (double *) calloc(N*P, sizeof(double));
                        ˜˜˜˜˜˜ ˜^˜
glm_test.c:335:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    Ui = U = (double *) calloc(nc*P, sizeof(double));
                        ˜˜˜˜˜˜ ˜˜^˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c glm_test_R.c -o glm_test_R.o
glm_test_R.c:55:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sstype = TYPEOF(Snp_subset);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:155:35: 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:156:39: 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:157:38: 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:158:38: 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:159:40: 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:162:30: 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:269:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sntype = TYPEOF(snpNames);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:424:25: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE tests_type = TYPEOF(Tests);
           ˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:486:20: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int mallowed = N * REAL(MissAllow)[0];
      ˜˜˜˜˜˜˜˜   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
glm_test_R.c:490:36: 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:491:38: 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:492:38: 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:493:42: 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:494:40: 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:495:44: 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:496:39: 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:497:43: 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:500:30: 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:501:34: 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:592:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        len = strlen(testname);
            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
21 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c gzio.c -o gzio.o
gzio.c:308:40: warning: implicit conversion changes signedness: 'uInt' (aka 'unsigned int') to 'int' [-Wsign-conversion]
            s->transparent = s->stream.avail_in;
                           ˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
gzio.c:413:26: warning: implicit conversion loses integer precision: 'int' to 'Byte' (aka 'unsigned char') [-Wconversion]
        *next_out++ = s->back;
                    ˜ ˜˜˜^˜˜˜
gzio.c:798:20: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
            size = gzwrite(file, s->inbuf, size);
                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -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 -ggdb -O0 -Wall -pedantic -Wconversion -c ibs.c -o ibs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -Wall -pedantic -Wconversion -c inflate.c -o inflate.o
inflate.c:137:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    if (bits > 16 || state->bits + bits > 32) return Z_STREAM_ERROR;
                                 ˜ ^˜˜˜
inflate.c:139:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    state->hold += value << state->bits;
                ˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
inflate.c:140:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    state->bits += bits;
                ˜˜ ^˜˜˜
inflate.c:711:62: warning: implicit conversion loses integer precision: 'unsigned int' to 'Bytef' (aka 'unsigned char') [-Wconversion]
                        state->head->name[state->length++] = len;
                                                           ˜ ^˜˜
inflate.c:732:65: warning: implicit conversion loses integer precision: 'unsigned int' to 'Bytef' (aka 'unsigned char') [-Wconversion]
                        state->head->comment[state->length++] = len;
                                                              ˜ ^˜˜
inflate.c:1148:60: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    strm->data_type = state->bits + (state->last ? 64 : 0) +
                    ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -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 -ggdb -O0 -Wall -pedantic -Wconversion -c input.c -o input.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c inputNew.c -o inputNew.o
inputNew.c:336:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      int lfn = strlen(filename); 
          ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
inputNew.c:635:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int la = strlen(a), lb = strlen(b);
        ˜˜   ^˜˜˜˜˜˜˜˜
inputNew.c:635:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int la = strlen(a), lb = strlen(b);
                        ˜˜   ^˜˜˜˜˜˜˜˜
inputNew.c:663:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
  char cu = toupper(c);
       ˜˜   ^˜˜˜˜˜˜˜˜˜
inputNew.c:688:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    lenf = lenb = strlen(front);
                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
inputNew.c:709:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int lenx = strlen(xi);
        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜
inputNew.c:855:28: 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))     \
                                        ^
inputNew.c:855:28: 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 -ggdb -O0 -Wall -pedantic -Wconversion -c input_unsorted.c -o input_unsorted.o
input_unsorted.c:241:13: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
          *gtype = gt;
                 ˜ ^˜
input_unsorted.c:250:16: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
      *gtype = gt;
             ˜ ^˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ld_graphic_eps.c -o ld_graphic_eps.o
ld_graphic_eps.c:81:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_HEADER, strlen(EPS_HEADER), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:83:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_1, strlen(EPS_PROLOG_1), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:84:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_2, strlen(EPS_PROLOG_2), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:85:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_3, strlen(EPS_PROLOG_3), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:86:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_4, strlen(EPS_PROLOG_4), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:87:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_5, strlen(EPS_PROLOG_5), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:88:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_6, strlen(EPS_PROLOG_6), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:89:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_7, strlen(EPS_PROLOG_7), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:90:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_8, strlen(EPS_PROLOG_8), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:91:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_9, strlen(EPS_PROLOG_9), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:92:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_10, strlen(EPS_PROLOG_10), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:93:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_11, strlen(EPS_PROLOG_11), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:94:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_PROLOG_12, strlen(EPS_PROLOG_12), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:97:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_BODY, strlen(EPS_BODY), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ld_graphic_eps.c:122:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  junk = fwrite(EPS_ENDING, strlen(EPS_ENDING), 1, gh->fp);
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
15 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ld_with.c -o ld_with.o
ld_with.c:76:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(dprime), 0, cols * n_select * sizeof(double));
                          ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
ld_with.c:76:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(dprime), 0, cols * n_select * sizeof(double));
                          ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
ld_with.c:77:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(rmisc) , 0, cols * n_select * sizeof(double));
                          ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
ld_with.c:77:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(rmisc) , 0, cols * n_select * sizeof(double));
                          ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
ld_with.c:78:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(lod)   , 0, cols * n_select * sizeof(double));
                          ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
ld_with.c:78:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(lod)   , 0, cols * n_select * sizeof(double));
                          ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜ ˜
/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 -ggdb -O0 -Wall -pedantic -Wconversion -c mla.c -o mla.o
mla.c:28:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    swy = (double *) calloc(nstrata, sizeof(double));
                     ˜˜˜˜˜˜ ^˜˜˜˜˜˜
mla.c:29:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    swt =  (double *) calloc(nstrata, sizeof(double));
                      ˜˜˜˜˜˜ ^˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -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 -ggdb -O0 -Wall -pedantic -Wconversion -c pairwise_linkage.c -o pairwise_linkage.o
pairwise_linkage.c:133:27: warning: 'memset' call operates on objects of type 'int' while the size is based on a different type 'int *' [-Wsizeof-pointer-memaccess]
  memset(count, 0, sizeof(count));
         ˜˜˜˜˜            ^˜˜˜˜
pairwise_linkage.c:133:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)?
  memset(count, 0, sizeof(count));
                          ^˜˜˜˜
pairwise_linkage.c:174:27: warning: 'memset' call operates on objects of type 'int' while the size is based on a different type 'int *' [-Wsizeof-pointer-memaccess]
  memset(count, 0, sizeof(count));
         ˜˜˜˜˜            ^˜˜˜˜
pairwise_linkage.c:174:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)?
  memset(count, 0, sizeof(count));
                          ^˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c read_chiamo.c -o read_chiamo.o
read_chiamo.c:71:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
  float f_threshold = 0.9;
        ˜˜˜˜˜˜˜˜˜˜˜   ^˜˜
read_chiamo.c:89:17: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
  f_threshold = REAL(threshold)[0];
              ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
read_chiamo.c:153:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  char *current_line = malloc(line_buffer_size);
                       ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
read_chiamo.c:196:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    cur_content_ptr->snps = (char *)calloc(sizeof(char), n_samples);
                                    ˜˜˜˜˜˜               ^˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c read_hapmap.c -o read_hapmap.o
read_hapmap.c:107:34: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
  int a_offset = strlen(alleles) - 2;
      ˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
read_hapmap.c:268:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  if (strncmp(current_line, HEADER_BEGINNING, header_skip)) {
      ˜˜˜˜˜˜˜                                 ^˜˜˜˜˜˜˜˜˜˜
read_hapmap.c:271:53: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    if (strncmp(current_line, HEADER_BEGINNING_ALT, header_skip)) {
        ˜˜˜˜˜˜˜                                     ^˜˜˜˜˜˜˜˜˜˜
read_hapmap.c:350:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    cur_content_ptr->snps = (char *)calloc(sizeof(char), n_samples);
                                    ˜˜˜˜˜˜               ^˜˜˜˜˜˜˜˜
read_hapmap.c:385:28: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
        unsigned char a = guesses >> 8;
                      ˜   ˜˜˜˜˜˜˜˜^˜˜˜
read_hapmap.c:400:25: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
      unsigned char a = *line_ptr++;
                    ˜   ^˜˜˜˜˜˜˜˜˜˜
read_hapmap.c:401:25: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
      unsigned char b = *line_ptr++;
                    ˜   ^˜˜˜˜˜˜˜˜˜˜
read_hapmap.c:402:27: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
      if (!expected_gtype(a) || !expected_gtype(b)) {
           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
read_hapmap.c:402:49: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
      if (!expected_gtype(a) || !expected_gtype(b)) {
                                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
read_hapmap.c:478:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    INTEGER(supp_pos)[i_snps] = cur_content_ptr->pos;
                              ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
10 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c read_pedfile.c -o read_pedfile.o
read_pedfile.c:150:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  char *current_line = malloc(line_buffer_size);
                       ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
read_pedfile.c:152:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  char *snp_summary = calloc(n_snps + 3,1);
                      ˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜
read_pedfile.c:196:65: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    cur_content_ptr->snps = (char *)calloc(sizeof(char), n_snps + 3);
                                    ˜˜˜˜˜˜               ˜˜˜˜˜˜˜^˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c read_signals.c -o read_signals.o
read_signals.c:50:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  char *line_buffer = (char *)malloc(buffersize);
                              ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -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 -ggdb -O0 -Wall -pedantic -Wconversion -c sdfpw.c -o sdfpw.o
sdfpw.c:400:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(dprime), 0, width * i_depth * sizeof(double));
                          ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
sdfpw.c:400:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(dprime), 0, width * i_depth * sizeof(double));
                          ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
sdfpw.c:401:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(rmisc) , 0, width * i_depth * sizeof(double));
                          ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
sdfpw.c:401:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(rmisc) , 0, width * i_depth * sizeof(double));
                          ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
sdfpw.c:402:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(lod)   , 0, width * i_depth * sizeof(double));
                          ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
sdfpw.c:402:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(REAL(lod)   , 0, width * i_depth * sizeof(double));
                          ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/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 -ggdb -O0 -Wall -pedantic -Wconversion -c single_snp_tests.c -o single_snp_tests.o
single_snp_tests.c:36:20: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE stype = TYPEOF(Stratum);
           ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
single_snp_tests.c:90:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sutype = TYPEOF(Subset);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜
single_snp_tests.c:105:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sstype = TYPEOF(Snp_subset);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
single_snp_tests.c:150:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    double **UV = (double **) calloc(nstrata, sizeof(double *));
                              ˜˜˜˜˜˜ ^˜˜˜˜˜˜
single_snp_tests.c:217:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    double **UVM = (double **) calloc(nstrata, sizeof(double *));
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜
single_snp_tests.c:218:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    double **UVF = (double **) calloc(nstrata, sizeof(double *));
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜
single_snp_tests.c:316:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
  SEXPTYPE sntype = TYPEOF(snpNames);
           ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c snp_summary.c -o snp_summary.o
snp_summary.c:96:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  int *obs = (int *) R_alloc(N, sizeof(int));
                     ˜˜˜˜˜˜˜ ^
snp_summary.c:131:18: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    calls[j] = nv+ny;
             ˜ ˜˜^˜˜
snp_summary.c:132:23: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    calls_female[j] = nv;
                    ˜ ^˜
snp_summary.c:233:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  int *obs = (int *) R_alloc(N, sizeof(int));
                     ˜˜˜˜˜˜˜ ^
snp_summary.c:259:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    calls[j] = nv;
             ˜ ^˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c snpmpy.c -o snpmpy.o
snpmpy.c:83:25: 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:83:25: 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:201:25: 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:201:25: 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))
                                     ^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -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 -ggdb -O0 -Wall -pedantic -Wconversion -c solve_quadratic.c -o solve_quadratic.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c structure.c -o structure.o
structure.c:89:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    Ti = (int *) calloc(N, sizeof(int));
                 ˜˜˜˜˜˜ ^
structure.c:90:22: 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:90:22: 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:91:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    Tk = (int *) calloc(M, sizeof(int));
                 ˜˜˜˜˜˜ ^
structure.c:92:22: 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:92:22: 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:110:25: 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:110:25: 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:340:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, N*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:340:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(result, 0x00, N*N*sizeof(int));
                       ˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
structure.c:417:24: 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:417:24: 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))
                                     ^
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c trees.c -o trees.o
trees.c:527:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        s->opt_len += (ulg)f * (bits + xbits);
                             ˜  ˜˜˜˜˜^˜˜˜˜˜˜
trees.c:528:60: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        if (stree) s->static_len += (ulg)f * (stree[n].Len + xbits);
                                           ˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
trees.c:561:31: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
                              *(long)tree[m].Freq;
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:591:60: 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:604:24: 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:773:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            do { send_code(s, curlen, s->bl_tree); } while (--count != 0);
                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:773:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            do { send_code(s, curlen, s->bl_tree); } while (--count != 0);
                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:777:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_code(s, curlen, s->bl_tree); count--;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:777:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_code(s, curlen, s->bl_tree); count--;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:780:13: 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:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:780:13: 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:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:780:48: 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:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:780:48: 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:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:783:13: 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:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:783:13: 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:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:783:50: 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:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:783:50: 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:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:786:13: 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:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:786:13: 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:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:786:52: 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:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:786:52: 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:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:826:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    s->opt_len += 3*(max_blindex+1) + 5+5+4;
               ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
trees.c:848:5: 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:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:848:5: 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:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:849:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, dcodes-1,   5);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:849:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, dcodes-1,   5);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:850:5: 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:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:850:5: 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:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:853:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, s->bl_tree[bl_order[rank]].Len, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:853:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, s->bl_tree[bl_order[rank]].Len, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:873:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, (STORED_BLOCK<<1)+eof, 3);  /* send block type */
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:873:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, (STORED_BLOCK<<1)+eof, 3);  /* send block type */
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:895:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, STATIC_TREES<<1, 3);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:895:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_bits(s, STATIC_TREES<<1, 3);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:896:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_code(s, END_BLOCK, static_ltree);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:896:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_code(s, END_BLOCK, static_ltree);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:907:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, STATIC_TREES<<1, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:907:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, STATIC_TREES<<1, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:908:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_code(s, END_BLOCK, static_ltree);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:908:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_code(s, END_BLOCK, static_ltree);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:988:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, (STATIC_TREES<<1)+eof, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:988:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, (STATIC_TREES<<1)+eof, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:994:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, (DYN_TREES<<1)+eof, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:994:9: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        send_bits(s, (DYN_TREES<<1)+eof, 3);
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1087:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, lc, ltree); /* send a literal byte */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1087:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, lc, ltree); /* send a literal byte */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1092:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, code+LITERALS+1, ltree); /* send the length code */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1092:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, code+LITERALS+1, ltree); /* send the length code */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1096:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_bits(s, lc, extra);       /* send the extra length bits */
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1096:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_bits(s, lc, extra);       /* send the extra length bits */
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1102:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, code, dtree);       /* send the distance code */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1102:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            send_code(s, code, dtree);       /* send the distance code */
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1105:25: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
                dist -= base_dist[code];
                     ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:1106:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                send_bits(s, dist, extra);   /* send the extra distance bits */
                ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
trees.c:220:15: note: expanded from macro 'send_bits'
    int val = value;\
              ^
trees.c:1106:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_bits(s, dist, extra);   /* send the extra distance bits */
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1106:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                send_bits(s, dist, extra);   /* send the extra distance bits */
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1116:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_code(s, END_BLOCK, ltree);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:223:44: note: expanded from macro 'send_bits'
    s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
                                      ˜    ^
trees.c:1116:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    send_code(s, END_BLOCK, ltree);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:167:33: note: expanded from macro 'send_code'
#  define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
trees.c:224:20: note: expanded from macro 'send_bits'
    s->bi_valid += len - Buf_size;\
                   ^˜˜ ˜
trees.c:1217:21: warning: implicit conversion changes signedness: 'charf' (aka 'char') to 'Bytef' (aka 'unsigned char') [-Wsign-conversion]
        put_byte(s, *buf++);
        ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./deflate.h:268:57: 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 -ggdb -O0 -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 -ggdb -O0 -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 chopsticks.so adler32.o bind.o compress.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o trees.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/chopsticks.Rcheck/chopsticks/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chopsticks)

chopsticks.Rcheck/chopsticks-Ex.timings:

nameusersystemelapsed
X.snp-class0.3170.0240.344
X.snp.matrix-class0.1560.0230.179
epsout.ld.snp0.2940.0180.316
for.exercise1.5350.0891.650
ibs.stats0.2410.0390.280
ibsCount0.6140.0380.654
ibsDist0.4370.0270.472
ld.snp0.2670.0230.294
ld.with0.1610.0340.199
pair.result.ld.snp0.1280.0190.149
plot.snp.dprime0.4110.0440.462
qq.chisq0.0030.0020.005
read.HapMap.data0.0110.0170.028
read.snps.chiamo0.0020.0030.006
read.wtccc.signals0.0050.0090.014
row.summary0.1850.0210.213
single.snp.tests0.1390.0220.165
snp-class0.0020.0050.007
snp.cbind0.4010.1440.557
snp.cor1.8100.0451.890
snp.dprime-class0.1540.0510.209
snp.lhs.tests0.1870.0370.228
snp.matrix-class0.3250.0580.389
snp.pre0.2520.0410.298
snp.rhs.tests0.1350.0260.167
testdata0.2310.0300.262
xxt1.6330.0351.669