>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rGADEM.buildbin-libdir rGADEM_2.8.0.tar.gz'
>>>>>>>
* installing *source* package 'rGADEM' ...
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for clang option to support OpenMP... unsupported
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... yes
checking dispatch/dispatch.h presence... yes
checking for dispatch/dispatch.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
config.status: src/config.h is unchanged
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c:230:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
useChIPscore=NUMERIC_VALUE(RuseChIPscore);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:114:26: note: expanded from macro 'NUMERIC_VALUE'
#define NUMERIC_VALUE(x) asReal(x)
^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:947:18: note: expanded from macro 'asReal'
#define asReal Rf_asReal
^
Gadem_Analysis.c:239:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
weightType=NUMERIC_VALUE(RweightType);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:114:26: note: expanded from macro 'NUMERIC_VALUE'
#define NUMERIC_VALUE(x) asReal(x)
^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:947:18: note: expanded from macro 'asReal'
#define asReal Rf_asReal
^
Gadem_Analysis.c:624:83: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
pwmConsensus[ii], scoreCutoff+ii, sdyad[ii], ii),
^˜
./config.h:35:45: note: expanded from macro 'DO_APPLY'
^(size_t counter_name) { task; });
^
Gadem_Analysis.c:625:16: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
populationSize, ii);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./config.h:33:20: note: expanded from macro 'DO_APPLY'
dispatch_apply(n_times, \
^
Gadem_Analysis.c:268:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len=strlen(seq[i]);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Gadem_Analysis.c:699:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
for (int j=strlen(sdyad[fitness[i].index]); j<maxSpaceWidth+10; j++) printf(" ");
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Gadem_Analysis.c:701:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
for (int j=strlen(sdyad[fitness[i].index]); j<maxSpaceWidth+10; j++) printf(" ");
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Gadem_Analysis.c:1350:31: warning: ordered comparison between pointer and zero ('char *' and 'int') is an extension [-Wpedantic]
if (fgets(buffer,250,fp)>0) {
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
Gadem_Analysis.c:1352:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len=strlen(buffer);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c align_sites.c -o align_sites.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c alloc.c -o alloc.o
alloc.c:18:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(double **)calloc(size1,sizeof(double *));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:21:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp[0]=(double *)calloc(size1*size2,sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜
alloc.c:35:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(char **)calloc(size1,sizeof(char *));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:38:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp[0]=(char *)calloc(size1*size2,sizeof(char));
˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜
alloc.c:52:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(int **)calloc(size1,sizeof(int *));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:55:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp[0]=(int *)calloc(size1*size2,sizeof(int));
˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜
alloc.c:67:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(char *)calloc(size1,sizeof(char));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:75:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(int *)calloc(size1,sizeof(int));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:83:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(double *)calloc(size1,sizeof(double));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:93:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp =(double ***)calloc(num_niche,sizeof(double **));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
alloc.c:94:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp[0] =(double **) calloc(num_niche*pop_size,sizeof(double *));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
alloc.c:95:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp[0][0]=(double *) calloc(num_niche*pop_size*size,sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
alloc.c:113:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp =(int ***)calloc(num_niche,sizeof(int **));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
alloc.c:114:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp[0] =(int **) calloc(num_niche*pop_size,sizeof(int *));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
alloc.c:115:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp[0][0]=(int *) calloc(num_niche*pop_size*size,sizeof(int));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
alloc.c:132:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(Fitness *)calloc(size1,sizeof(Fitness));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:141:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(Wheel *)calloc(size1,sizeof(Wheel));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:150:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(Sites *)calloc(size1,sizeof(Sites));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:160:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(Sites **)calloc(size1,sizeof(Sites *));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:163:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp[0]=(Sites *)calloc(size1*size2,sizeof(Sites));
˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜
alloc.c:177:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(Chrs **)calloc(size1,sizeof(Chrs *));
˜˜˜˜˜˜ ^˜˜˜˜
alloc.c:180:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp[0]=(Chrs *)calloc(size1*size2,sizeof(Chrs));
˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜
alloc.c:194:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(Words *)calloc(numCategory,sizeof(Words));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
alloc.c:223:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp=(Ktuples *)calloc(numKmer,sizeof(Ktuples));
˜˜˜˜˜˜ ^˜˜˜˜˜˜
alloc.c:232:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
llDist=(Pgfs *)calloc(size,sizeof(Pgfs));
˜˜˜˜˜˜ ^˜˜˜
25 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c background.c -o background.o
background.c:42:33: warning: ordered comparison between pointer and zero ('char *' and 'int') is an extension [-Wpedantic]
if ((fgets(buffer,256,fp))>0) {
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
background.c:44:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len=strlen(buffer);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
background.c:52:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len2=strlen(tok);
˜^˜˜˜˜˜˜˜˜˜˜
background.c:76:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len2=strlen(tok);
˜^˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c base_frequency.c -o base_frequency.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c check_convergence.c -o check_convergence.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c check_pwm_dist.c -o check_pwm_dist.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c consensus.c -o consensus.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c construct_pwm.c -o construct_pwm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c copy_pwm.c -o copy_pwm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c crossover.c -o crossover.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c effect_seq_len.c -o effect_seq_len.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c evalue_meme.c -o evalue_meme.o
evalue_meme.c:153:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
create_2array(IP, int, A, N+1);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:166:17: note: expanded from macro 'create_2array'
dbmalloc((v), _ir, typ *); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:153:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
create_2array(IP, int, A, N+1);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:171:19: note: expanded from macro 'create_2array'
dbmalloc(tmp, _ic, typ); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:154:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
create_2array(logP, double, A, N+1);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:166:17: note: expanded from macro 'create_2array'
dbmalloc((v), _ir, typ *); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:154:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
create_2array(logP, double, A, N+1);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:171:19: note: expanded from macro 'create_2array'
dbmalloc(tmp, _ic, typ); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:155:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(minI, N+1, int);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:155:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(minI, N+1, int);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:156:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(maxI, N+1, int);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:156:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(maxI, N+1, int);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:159:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
for (i=dd_sum=0; i<A; i++) dd_sum += dd[i] + EPSILON;
˜˜˜˜˜˜˜^˜
evalue_meme.c:169:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
for (i=min=0; i<A; i++) min += dd[i]*N*(log(dd[i]) - log(dd[i]));
˜˜˜˜^˜
evalue_meme.c:210:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
create_2array(logSP, double, N+1, Irange+1);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:166:17: note: expanded from macro 'create_2array'
dbmalloc((v), _ir, typ *); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:210:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
create_2array(logSP, double, N+1, Irange+1);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:171:19: note: expanded from macro 'create_2array'
dbmalloc(tmp, _ic, typ); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:227:38: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
int max = MAX(min, maxI[n-k] - (1-frac)*(maxI[n-k]-minI[n-k]+1));
˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:96:38: note: expanded from macro 'MAX'
#define MAX(X,Y) ((X) > (Y) ? (X) : (Y))
^
evalue_meme.c:250:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(prob, *range+2, double);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:250:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(prob, *range+2, double);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:286:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(d_sum, range+1, double); /* space for distribution */
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:286:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(d_sum, range+1, double); /* space for distribution */
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:325:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(cdf, r+1, double);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:325:3: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(cdf, r+1, double);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:393:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(distrs, N+1, DISTR); /* create array of distributions */
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:393:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(distrs, N+1, DISTR); /* create array of distributions */
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:410:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(distrs[N].d, w+1, double *);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:410:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(distrs[N].d, w+1, double *);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:411:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(distrs[N].cdf, w+1, double *);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:411:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(distrs[N].cdf, w+1, double *);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:412:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(distrs[N].offset, w+1, int);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:412:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(distrs[N].offset, w+1, int);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:413:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(distrs[N].range, w+1, int);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:413:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(distrs[N].range, w+1, int);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:520:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(len, nseqs, int);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:144:27: note: expanded from macro 'Resize'
myrealloc(new_P, (P), _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:134:42: note: expanded from macro 'myrealloc'
(P) = (T *) realloc((malloc_t)(OLDP), (N)*sizeof(T)); \
^
evalue_meme.c:520:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Resize(len, nseqs, int);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./evalue_meme.h:146:21: note: expanded from macro 'Resize'
dbmalloc(new_P, _n_, T); \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./evalue_meme.h:131:33: note: expanded from macro 'dbmalloc'
(P) = (N) > 0 ? (T *) malloc((N)*sizeof(T)) : NULL; \
^
evalue_meme.c:522:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort((char *) len, nseqs, sizeof(int), int_compare);
˜˜˜˜˜ ^˜˜˜˜
32 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c extend_alignment.c -o extend_alignment.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c initial_population.c -o initial_population.o
initial_population.c:81:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len0=strlen(word[dyad[i][0].wordGroup].s1[dyad[i][0].wordID]);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
initial_population.c:100:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len2=strlen(word[dyad[i][2].wordGroup].s1[dyad[i][2].wordID]);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mask_sites.c -o mask_sites.o
mask_sites.c:71:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while (strncmp(s1,kmer[l],klen)==0) {
˜˜˜˜˜˜˜ ^˜˜˜
mask_sites.c:109:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while (strncmp(s1,kmer[l],klen)==0) {
˜˜˜˜˜˜˜ ^˜˜˜
mask_sites.c:143:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while (strncmp(s1,kmer[l],klen)==0) {
˜˜˜˜˜˜˜ ^˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mutation.c -o mutation.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c normalization.c -o normalization.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c output.c -o output.o
output.c:24:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len=strlen(geneID[site[i].seq]);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c pwm_score_distr.c -o pwm_score_distr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c read_matrix.c -o read_matrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c read_pwm0.c -o read_pwm0.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c read_seq.c -o read_seq.o
read_seq.c:38:37: warning: ordered comparison between pointer and zero ('char *' and 'int') is an extension [-Wpedantic]
if (fgets(buffer,maxBufferLen,fp)>0) {
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
read_seq.c:40:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len=strlen(buffer);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
read_seq.c:50:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len=strlen(tok);
˜^˜˜˜˜˜˜˜˜˜˜
read_seq.c:90:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
len=strlen(buffer);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c reverse_seq.c -o reverse_seq.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sample_wo_replacement.c -o sample_wo_replacement.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c scan_sites.c -o scan_sites.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c score_subsequence.c -o score_subsequence.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c selection.c -o selection.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sort.c -o sort.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c top_kmers.c -o top_kmers.o
top_kmers.c:336:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (strncmp(s1,kmer[m],kmerLen)==0) { id[slide]=m; break; }
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
top_kmers.c:341:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (strncmp(s2,kmer[m],kmerLen)==0) { id[slide]=m; break; }
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c transform_pwm.c -o transform_pwm.o
transform_pwm.c:60:60: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
for (j=0; j<4; j++) ipwm[i][j]=DOUBLE_TO_INT_SCALE/4;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c weights.c -o weights.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 rGADEM.so Gadem_Analysis.o align_sites.o alloc.o background.o base_frequency.o check_convergence.o check_pwm_dist.o consensus.o construct_pwm.o copy_pwm.o crossover.o effect_seq_len.o evalue_meme.o extend_alignment.o initial_population.o mask_sites.o mutation.o normalization.o output.o pwm_score_distr.o read_matrix.o read_pwm0.o read_seq.o reverse_seq.o sample_wo_replacement.o scan_sites.o score_subsequence.o selection.o sort.o top_kmers.o transform_pwm.o weights.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rGADEM)
>>>>>>>
>>>>>>> FIXING LINKS FOR rGADEM.buildbin-libdir/rGADEM/libs//rGADEM.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "rGADEM.buildbin-libdir/rGADEM/libs//rGADEM.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "rGADEM.buildbin-libdir/rGADEM/libs//rGADEM.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "rGADEM.buildbin-libdir/rGADEM/libs//rGADEM.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "rGADEM.buildbin-libdir/rGADEM/libs//rGADEM.so"