Package: qpgraph

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qpgraph_1.16.0.tar.gz

StartedAt: 2013-05-01 09:43:13 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 09:49:11 -0700 (Wed, 01 May 2013)

EllapsedTime: 357.5 seconds

RetCode: 0

Status:  OK

CheckDir: qpgraph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/qpgraph.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 'qpgraph/DESCRIPTION' ... OK
* this is package 'qpgraph' version '1.16.0'
* 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 'qpgraph' can be installed ... [34s/36s] OK
* checking installed package size ... OK
* 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 ... OK
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [35s/36s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
qpAvgNrr 5.185   0.03   5.464
* 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

* installing *source* package 'qpgraph' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking build system type... i686-apple-darwin10.8.0
checking host system type... i686-apple-darwin10.8.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -Wall -pedantic -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cliquer.c -o cliquer.o
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:165:7: warning: implicit conversion changes signedness: 'int' to 'setelement' (aka 'unsigned long') [-Wsign-conversion]
        s[0]=size;
            ˜^˜˜˜
./set.h:200:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        s=Realloc(s-1, (n+1), setelement)+1;
          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                   ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:204:11: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                       (n-SET_ARRAY_LENGTH(s))*sizeof(setelement));
                        ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:204:11: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                       (n-SET_ARRAY_LENGTH(s))*sizeof(setelement));
                        ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:208:8: warning: implicit conversion changes signedness: 'int' to 'setelement' (aka 'unsigned long') [-Wsign-conversion]
        s[-1]=size;
             ˜^˜˜˜
./set.h:237:14: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        new=set_new(SET_MAX_SIZE(s));
            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./set.h:292:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:292:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:295:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:295:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:300:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MIN(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:59:30: note: expanded from macro 'MIN'
#define MIN(a,b) (((a)<(b))?(a):(b))
                             ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:300:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MIN(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:59:34: note: expanded from macro 'MIN'
#define MIN(a,b) (((a)<(b))?(a):(b))
                                 ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:325:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:325:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:328:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:328:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:333:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MAX(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:333:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MAX(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
cliquer.c:203:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                newtable=(int *) R_alloc(g->n, sizeof(int));
                                 ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:309:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                newtable=(int *) R_alloc(g->n, sizeof(int));
                                 ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:340:40: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                if (sub_unweighted_single(newtable,p1-newtable,
                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ˜˜^˜˜˜˜˜˜˜˜
cliquer.c:401:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                newtable=(int *) R_alloc(g->n, sizeof(int));
                                 ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:546:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                newtable=(int *) R_alloc(g->n, sizeof(int));
                                 ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:586:35: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                n=sub_unweighted_all(newtable,p1-newtable,
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ˜˜^˜˜˜˜˜˜˜˜
cliquer.c:702:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                newtable=(int *) R_alloc(g->n, sizeof(int));
                                 ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:808:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                newtable=(int *) R_alloc(g->n, sizeof(int));
                                 ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:948:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                newtable=(int *) R_alloc(g->n, sizeof(int));
                                 ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:982:41: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                prune_low=sub_weighted_all(newtable,p1-newtable,
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ˜˜^˜˜˜˜˜˜˜˜
cliquer.c:1099:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                table=(int *) R_alloc(g->n, sizeof(int));
                              ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:1224:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        clique_size=(int *) R_alloc(g->n, sizeof(int));
                            ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:1227:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        temp_list=(int **) R_alloc((g->n+2), sizeof(int *));
                           ˜˜˜˜˜˜˜  ˜˜˜˜^˜
cliquer.c:1218:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                clocks_per_sec=sysconf(_SC_CLK_TCK);
                              ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cliquer.c:1352:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        clique_size=(int *) R_alloc(g->n, sizeof(int));
                            ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:1355:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        temp_list=(int **) R_alloc((g->n+2), sizeof(int *));
                           ˜˜˜˜˜˜˜  ˜˜˜˜^˜
cliquer.c:1359:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(clique_size,0,g->n * sizeof(int));
                             ˜˜˜^ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
cliquer.c:1359:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(clique_size,0,g->n * sizeof(int));
                             ˜˜˜^ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
cliquer.c:1346:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                clocks_per_sec=sysconf(_SC_CLK_TCK);
                              ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cliquer.c:1526:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        clique_size=(int *) R_alloc(g->n, sizeof(int));
                            ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:1527:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(clique_size, 0, g->n * sizeof(int));
                               ˜˜˜^ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
cliquer.c:1527:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(clique_size, 0, g->n * sizeof(int));
                               ˜˜˜^ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
cliquer.c:1530:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        temp_list=(int **) R_alloc((g->n+2), sizeof(int *));
                           ˜˜˜˜˜˜˜  ˜˜˜˜^˜
cliquer.c:1499:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                clocks_per_sec=sysconf(_SC_CLK_TCK);
                              ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cliquer.c:1687:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        clique_size=(int *) R_alloc(g->n, sizeof(int));
                            ˜˜˜˜˜˜˜ ˜˜˜^
cliquer.c:1688:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(clique_size, 0, g->n * sizeof(int));
                               ˜˜˜^ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
cliquer.c:1688:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(clique_size, 0, g->n * sizeof(int));
                               ˜˜˜^ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
cliquer.c:1691:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        temp_list=(int **) R_alloc((g->n+2), sizeof(int *));
                           ˜˜˜˜˜˜˜  ˜˜˜˜^˜
cliquer.c:1661:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                clocks_per_sec=sysconf(_SC_CLK_TCK);
                              ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cliquer.c:1809:13: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                prev_time=realtime;
                         ˜^˜˜˜˜˜˜˜
cliquer.c:1788:8: warning: unused variable 'fp' [-Wunused-variable]
        FILE *fp=opts->output;
              ^
cliquer.c:1854:12: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
        prev_time=realtime;
                 ˜^˜˜˜˜˜˜˜
cliquer.c:1837:8: warning: unused variable 'fp' [-Wunused-variable]
        FILE *fp=opts->output;
              ^
51 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -Wall -pedantic -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c graph.c -o graph.o
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:165:7: warning: implicit conversion changes signedness: 'int' to 'setelement' (aka 'unsigned long') [-Wsign-conversion]
        s[0]=size;
            ˜^˜˜˜
./set.h:200:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        s=Realloc(s-1, (n+1), setelement)+1;
          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                   ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:204:11: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                       (n-SET_ARRAY_LENGTH(s))*sizeof(setelement));
                        ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:204:11: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                       (n-SET_ARRAY_LENGTH(s))*sizeof(setelement));
                        ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:208:8: warning: implicit conversion changes signedness: 'int' to 'setelement' (aka 'unsigned long') [-Wsign-conversion]
        s[-1]=size;
             ˜^˜˜˜
./set.h:237:14: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        new=set_new(SET_MAX_SIZE(s));
            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./set.h:292:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:292:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:295:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:295:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:300:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MIN(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:59:30: note: expanded from macro 'MIN'
#define MIN(a,b) (((a)<(b))?(a):(b))
                             ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:300:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MIN(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:59:34: note: expanded from macro 'MIN'
#define MIN(a,b) (((a)<(b))?(a):(b))
                                 ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:325:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:325:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:328:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:328:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:333:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MAX(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:333:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MAX(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
graph.c:48:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        g->edges=(set_t *) R_alloc(g->n, sizeof(set_t));
                           ˜˜˜˜˜˜˜ ˜˜˜^
graph.c:50:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        g->weights=(int *) R_alloc(g->n, sizeof(int));
                           ˜˜˜˜˜˜˜ ˜˜˜^
graph.c:103:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        g->edges=Realloc(g->edges, size, set_t);
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                   ^
graph.c:114:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        g->weights=Realloc(g->weights, size, int);
                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                   ^
22 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -Wall -pedantic -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c qpgraph.c -o qpgraph.o
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:165:7: warning: implicit conversion changes signedness: 'int' to 'setelement' (aka 'unsigned long') [-Wsign-conversion]
        s[0]=size;
            ˜^˜˜˜
./set.h:200:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        s=Realloc(s-1, (n+1), setelement)+1;
          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                   ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:204:11: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                       (n-SET_ARRAY_LENGTH(s))*sizeof(setelement));
                        ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:204:11: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                       (n-SET_ARRAY_LENGTH(s))*sizeof(setelement));
                        ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:208:8: warning: implicit conversion changes signedness: 'int' to 'setelement' (aka 'unsigned long') [-Wsign-conversion]
        s[-1]=size;
             ˜^˜˜˜
./set.h:237:14: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        new=set_new(SET_MAX_SIZE(s));
            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./set.h:292:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:292:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:295:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:295:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:300:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MIN(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:59:30: note: expanded from macro 'MIN'
#define MIN(a,b) (((a)<(b))?(a):(b))
                             ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:300:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MIN(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:59:34: note: expanded from macro 'MIN'
#define MIN(a,b) (((a)<(b))?(a):(b))
                                 ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:325:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:325:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:328:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:328:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:333:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MAX(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from qpgraph.c:32:
In file included from ./cliquer.h:7:
./set.h:333:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MAX(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
qpgraph.c:2154:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          memset(S, 0, sizeof(double) * n_upper_tri);
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:2154:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          memset(S, 0, sizeof(double) * n_upper_tri);
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:2238:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memset(S, 0, sizeof(double) * n_upper_tri);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:2238:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memset(S, 0, sizeof(double) * n_upper_tri);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:2320:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memset(S, 0, sizeof(double) * n_upper_tri);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:2320:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memset(S, 0, sizeof(double) * n_upper_tri);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:2683:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memset(S, 0, sizeof(double) * n_upper_tri);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:2683:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memset(S, 0, sizeof(double) * n_upper_tri);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:2768:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memset(S, 0, sizeof(double) * n_upper_tri);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:2768:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memset(S, 0, sizeof(double) * n_upper_tri);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:2850:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          memset(S, 0, sizeof(double) * n_upper_tri);
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:2850:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          memset(S, 0, sizeof(double) * n_upper_tri);
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:3675:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(ssd_mat, 0, ((n_Y_i * (n_Y_i + 1)) / 2) * sizeof(double));
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:3675:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(ssd_mat, 0, ((n_Y_i * (n_Y_i + 1)) / 2) * sizeof(double));
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:3726:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(ssd_mat, 0, ((n_Y_j * (n_Y_j + 1)) / 2) * sizeof(double));
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:3726:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(ssd_mat, 0, ((n_Y_j * (n_Y_j + 1)) / 2) * sizeof(double));
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:3777:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(ssd_mat, 0, ((n_Y_j * (n_Y_j + 1)) / 2) * sizeof(double));
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:3777:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(ssd_mat, 0, ((n_Y_j * (n_Y_j + 1)) / 2) * sizeof(double));
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:3887:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(obs_idx, n_obs, sizeof(int), indirect_int_cmp);
    ˜˜˜˜˜          ^˜˜˜˜
qpgraph.c:4105:19: warning: unused variable 'k' [-Wunused-variable]
  int         i,j,k;
                  ^
qpgraph.c:4105:15: warning: unused variable 'i' [-Wunused-variable]
  int         i,j,k;
              ^
qpgraph.c:4105:17: warning: unused variable 'j' [-Wunused-variable]
  int         i,j,k;
                ^
qpgraph.c:4147:15: warning: unused variable 'Y_j' [-Wunused-variable]
  int*        Y_j = NULL;
              ^
qpgraph.c:4747:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(ssd_mat, 0, ((n_Y_i * (n_Y_i + 1)) / 2) * sizeof(double));
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:4747:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(ssd_mat, 0, ((n_Y_i * (n_Y_i + 1)) / 2) * sizeof(double));
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:4796:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(ssd_mat, 0, ((n_Y_j * (n_Y_j + 1)) / 2) * sizeof(double));
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:4796:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(ssd_mat, 0, ((n_Y_j * (n_Y_j + 1)) / 2) * sizeof(double));
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:4846:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(ssd_mat, 0, ((n_Y_j * (n_Y_j + 1)) / 2) * sizeof(double));
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:4846:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(ssd_mat, 0, ((n_Y_j * (n_Y_j + 1)) / 2) * sizeof(double));
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:4956:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(S, 0, sizeof(double) * n_upper_tri);
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:4956:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(S, 0, sizeof(double) * n_upper_tri);
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:5751:14: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  qsort(deg, n, sizeof(IntWithIdx), int_cmp_desc_idx_decr);
  ˜˜˜˜˜      ^
qpgraph.c:6288:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
              idxclqs[v] = (int *) Realloc(idxclqs[v],sidxclqs[v],int);
                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                   ^
qpgraph.c:6313:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        qsort(idxclqs[i],nidxclqs[i],sizeof(int),int_cmp);
        ˜˜˜˜˜            ^˜˜˜˜˜˜˜˜˜˜
qpgraph.c:6384:81: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    if (bsearch(INTEGER(VECTOR_ELT(clqlstR,v))+i,INTEGER(VECTOR_ELT(clqlstR,w)),nclqs_w,sizeof(int),int_cmp))
        ˜˜˜˜˜˜˜                                                                 ^˜˜˜˜˜˜
qpgraph.c:6389:18: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  qsort(clqs_v_w,nclqs_v_w,sizeof(int),int_cmp);
  ˜˜˜˜˜          ^˜˜˜˜˜˜˜˜
qpgraph.c:6504:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          idxclqs[v] = (int *) Realloc(idxclqs[v],sidxclqs[v],int);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                   ^
qpgraph.c:6536:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(idxclqs[i],nidxclqs[i],sizeof(int),int_cmp);
    ˜˜˜˜˜            ^˜˜˜˜˜˜˜˜˜˜
qpgraph.c:6914:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  Memcpy(Vn,Vf,(size_t) n*n);
                         ˜^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:70:47: note: expanded from macro 'Memcpy'
#define Memcpy(p,q,n)  memcpy( p, q, (size_t)(n) * sizeof(*p) )
                                              ^
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:6914:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  Memcpy(Vn,Vf,(size_t) n*n);
                         ˜^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:70:47: note: expanded from macro 'Memcpy'
#define Memcpy(p,q,n)  memcpy( p, q, (size_t)(n) * sizeof(*p) )
                                              ^
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
qpgraph.c:7038:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(beta, 0, (n_var-1) * sizeof(double));
                       ˜˜˜˜˜^˜  ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:7038:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      memset(beta, 0, (n_var-1) * sizeof(double));
                       ˜˜˜˜˜^˜  ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:7195:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(inv, 0, 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))     \
                                        ^
qpgraph.c:7195:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(inv, 0, n * n * sizeof(double));
                   ˜˜^˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:7449:12: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
  *e_i = 1 + (unsigned int) (-0.5 + sqrt(0.25 + 2.0 * ((double) i)));
       ˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
qpgraph.c:7450:12: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
  *e_j = i - (unsigned int) ((double) ((*e_i)*((*e_i)-1)) / 2.0);
       ˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
qpgraph.c:7450:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  *e_j = i - (unsigned int) ((double) ((*e_i)*((*e_i)-1)) / 2.0);
         ^ ˜
qpgraph.c:7606:16: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
    meanv[i] = tmp;
             ˜ ^˜˜
qpgraph.c:7746:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(ssd_val, 0, sizeof(double) * n_upper_tri);
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:7746:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(ssd_val, 0, sizeof(double) * n_upper_tri);
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:7860:18: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  qsort(obs_idx, n_obs, sizeof(int), indirect_int_cmp);
  ˜˜˜˜˜          ^˜˜˜˜
qpgraph.c:7831:17: warning: unused variable 'm' [-Wunused-variable]
  int     i,j,k,m;
                ^
qpgraph.c:7831:15: warning: unused variable 'k' [-Wunused-variable]
  int     i,j,k,m;
              ^
qpgraph.c:7909:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  return ib->x - ia->x;
  ˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜
qpgraph.c:7960:5: warning: incompatible pointer types assigning to 'Rboolean *' from 'int *' [-Wincompatible-pointer-types]
  G = LOGICAL(GR);
    ^ ˜˜˜˜˜˜˜˜˜˜˜
qpgraph.c:7976:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(G, FALSE, sizeof(Rboolean) * n_upper_tri);
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
qpgraph.c:7976:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(G, FALSE, sizeof(Rboolean) * n_upper_tri);
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
qpgraph.c:7988:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      qsort(working_deg, p, sizeof(IntWithIdx), int_cmp_desc_idx_incr);
      ˜˜˜˜˜              ^
qpgraph.c:8053:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            qsort(cdf, (n_vtx_left*(n_vtx_left-1))/2, sizeof(DblWithIdx), dbl_cmp_desc_idx_decr);
            ˜˜˜˜˜      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
77 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -Wall -pedantic -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c reorder.c -o reorder.o
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:165:7: warning: implicit conversion changes signedness: 'int' to 'setelement' (aka 'unsigned long') [-Wsign-conversion]
        s[0]=size;
            ˜^˜˜˜
./set.h:200:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        s=Realloc(s-1, (n+1), setelement)+1;
          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                   ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:204:11: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                       (n-SET_ARRAY_LENGTH(s))*sizeof(setelement));
                        ^˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:204:11: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                       (n-SET_ARRAY_LENGTH(s))*sizeof(setelement));
                        ^˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:208:8: warning: implicit conversion changes signedness: 'int' to 'setelement' (aka 'unsigned long') [-Wsign-conversion]
        s[-1]=size;
             ˜^˜˜˜
./set.h:237:14: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        new=set_new(SET_MAX_SIZE(s));
            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./set.h:292:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:292:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:295:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:295:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:300:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MIN(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:59:30: note: expanded from macro 'MIN'
#define MIN(a,b) (((a)<(b))?(a):(b))
                             ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:300:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MIN(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:59:34: note: expanded from macro 'MIN'
#define MIN(a,b) (((a)<(b))?(a):(b))
                                 ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:325:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:325:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:328:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:328:37: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
                      ˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:333:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MAX(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:62:30: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                             ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:333:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        max=MAX(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
           ˜                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:147:53: note: expanded from macro 'SET_ARRAY_LENGTH'
#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./misc.h:62:34: note: expanded from macro 'MAX'
#define MAX(a,b) (((a)>(b))?(a):(b))
                                 ^
reorder.c:42:43: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        ASSERT(reorder_is_bijection(order,SET_MAX_SIZE(s)));
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
./misc.h:43:15: note: expanded from macro 'ASSERT'
        if (!(expr)) { \
              ^
reorder.c:44:21: warning: implicit conversion loses integer precision: 'setelement' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        tmp=set_new(SET_MAX_SIZE(s));
            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./set.h:145:26: note: expanded from macro 'SET_MAX_SIZE'
#define SET_MAX_SIZE(s) ((s)[-1])
                         ^˜˜˜˜˜˜
reorder.c:86:31: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        tmp=(set_t *) R_alloc((long) g->n, sizeof(set_t));
                      ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
reorder.c:109:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        new=(int *) R_alloc(n, sizeof(int));
                    ˜˜˜˜˜˜˜ ^
reorder.c:110:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(new,order,n*sizeof(int));
                         ^˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
reorder.c:110:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(new,order,n*sizeof(int));
                         ^˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
reorder.c:128:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        new=(int *) R_alloc(n, sizeof(int));
                    ˜˜˜˜˜˜˜ ^
reorder.c:195:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        order=(int *) R_alloc(n, sizeof(int));
                      ˜˜˜˜˜˜˜ ^
reorder.c:224:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        order=(int *) R_alloc(g->n, sizeof(int));
                      ˜˜˜˜˜˜˜ ˜˜˜^
reorder.c:279:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(tmp_used,0,g->n * sizeof(boolean));
                                  ˜˜˜^ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
reorder.c:279:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(tmp_used,0,g->n * sizeof(boolean));
                                  ˜˜˜^ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
reorder.c:335:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        nwt=(int *) R_alloc(g->n, sizeof(int));
                    ˜˜˜˜˜˜˜ ˜˜˜^
reorder.c:337:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        order=(int *) R_alloc(g->n, sizeof(int));
                      ˜˜˜˜˜˜˜ ˜˜˜^
reorder.c:442:18: warning: implicit conversion changes signedness: 'time_t' (aka 'long') to 'unsigned long' [-Wsign-conversion]
        srand(times(&t)+time(NULL));
                       ˜^˜˜˜˜˜˜˜˜˜
reorder.c:442:17: warning: implicit conversion loses integer precision: 'unsigned long' to 'unsigned int' [-Wshorten-64-to-32]
        srand(times(&t)+time(NULL));
        ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
33 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/qpgraph.Rcheck/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function from function 'rmvnorm' in package 'qpgraph'
Creating a generic function from function 'sim.cross' in package 'qpgraph'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qpgraph)

name	user	system	elapsed
EcoliOxygen	0.477	0.008	0.502
qpAllCItests	0.324	0.016	0.346
qpAnyGraph	0.188	0.014	0.203
qpAvgNrr	5.185	0.030	5.464
qpBoundary	1.03	0.01	1.05
qpCItest	0.069	0.010	0.080
qpClique	1.041	0.014	1.066
qpCliqueNumber	0.976	0.038	1.018
qpCov	0.173	0.021	0.198
qpEdgeNrr	0.077	0.014	0.092
qpFunctionalCoherence	0.033	0.017	0.050
qpG2Sigma	0.037	0.008	0.047
qpGenNrr	1.884	0.030	1.944
qpGetCliques	0.858	0.017	0.885
qpGraph	0.667	0.014	0.681
qpGraphDensity	1.030	0.014	1.055
qpHTF	0.222	0.020	0.244
qpHist	0.706	0.010	0.716
qpIPF	0.389	0.018	0.409
qpK2ParCor	0.069	0.010	0.079
qpNrr	0.549	0.014	0.564
qpPAC	1.439	0.043	1.495
qpPCC	0.201	0.014	0.230
qpPRscoreThreshold	0.486	0.011	0.504
qpPlotMap	0.154	0.031	0.187
qpPlotNetwork	0.228	0.012	0.249
qpPrecisionRecall	0.721	0.018	0.744
qpRndGraph	0.029	0.006	0.048
qpRndHMGM	0.010	0.004	0.019
qpRndWishart	0.042	0.013	0.054
qpSampleFromHMGM	0.011	0.003	0.027
qpTopPairs	0.014	0.003	0.018
qpUnifRndAssociation	0.018	0.003	0.021
qpUpdateCliquesRemoving	0.021	0.008	0.029