beadarray 2.10.0
Mark Dunning
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/beadarray | | Last Changed Rev: 75263 / Revision: 76155 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=beadarray.buildbin-libdir beadarray_2.10.0.tar.gz'
>>>>>>>
* installing *source* package 'beadarray' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c BASH.c -o BASH.o
BASH.c:81:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *margined = (int *) R_alloc(*no, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜
BASH.c:82:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *windowed = (int *) R_alloc(*no, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜
BASH.c:202:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *invaded = (int *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(int) ); //must be big enough to contain IDs of all invaded nodes
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:203:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *invadedE = (double *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:204:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *done = (int *) R_alloc(*nbeads, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
BASH.c:206:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(done, 0, sizeof(int) * *nbeads);
˜ ^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
BASH.c:206:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(done, 0, sizeof(int) * *nbeads);
˜ ^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
BASH.c:306:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *invaded = (int *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(int) ); //must be big enough to contain IDs of all invaded nodes
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:307:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *invadedE = (double *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(double) );
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:308:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *invadedW = (double *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(double) );
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:310:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *done = (int *) R_alloc(*nbeads, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
BASH.c:312:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(done, 0, *nbeads * sizeof(int));
^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
BASH.c:312:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(done, 0, *nbeads * sizeof(int));
^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
BASH.c:441:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *done = (int *) R_alloc(*nbeads, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
BASH.c:442:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(done, 0, *nbeads * sizeof(int));
^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
BASH.c:442:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(done, 0, *nbeads * sizeof(int));
^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
BASH.c:445:56: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *choose = (double *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(double) );
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:446:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *thresh = (int *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(int) );
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:470:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *outlier = (int *) R_alloc(*nbeads, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
BASH.c:582:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *done = (int *) R_alloc(*nbeads, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
BASH.c:583:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *marker = (int *) R_alloc((*invasions + 1), sizeof(int));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
BASH.c:587:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(done, 0, *nbeads * sizeof(int));
^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
BASH.c:587:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(done, 0, *nbeads * sizeof(int));
^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
23 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c HULK.c -o HULK.o
HULK.c:14:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *done = (int *) R_alloc(*nbeads, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
HULK.c:15:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(done, 0, *nbeads * sizeof(int));
^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
HULK.c:15:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(done, 0, *nbeads * sizeof(int));
^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
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 determiningGridPositions.c -o determiningGridPositions.o
determiningGridPositions.c:105:20: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
tmpInt = 2 * pow(0, col % 2);
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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 findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c:22:29: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
mid = floor((right-left)/2)+left;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
findAllOutliers.c:88:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tempArr = (double *) R_alloc(length, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜
findAllOutliers.c:95:6: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
i = floor(length/2);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
findAllOutliers.c:111:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *arr2 = (double *) R_alloc(length, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜
findAllOutliers.c:163:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
inten = (double *) R_alloc(*count, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜
findAllOutliers.c:192:25: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
nsize1 = (sizeof(int) * (i+1));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
findAllOutliers.c:192:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
nsize1 = (sizeof(int) * (i+1));
˜ ˜^˜
findAllOutliers.c:193:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
validInds = (int *)realloc(validInds, nsize1);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
findAllOutliers.c:201:26: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
nsize1 = (sizeof(int) * (i+1));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
findAllOutliers.c:201:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
nsize1 = (sizeof(int) * (i+1));
˜ ˜^˜
findAllOutliers.c:202:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
validInds = (int *)realloc(validInds, nsize1);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
findAllOutliers.c:208:26: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
nsize2 = (sizeof(int) * (j+1));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
findAllOutliers.c:208:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
nsize2 = (sizeof(int) * (j+1));
˜ ˜^˜
findAllOutliers.c:209:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
outlierInds = (int *)realloc(outlierInds, nsize2);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imageProcessing.c -o imageProcessing.o
imageProcessing.c:43:38: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
M[count++] = REAL(pixelMatrix)[tmp + k];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
imageProcessing.c:88:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
^
imageProcessing.c:135:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
^
imageProcessing.c:244:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
^
imageProcessing.c:251:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
^
imageProcessing.c:282:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
for(i = x - 3.5; i <= x + 3.5; i++) {
˜ ˜˜^˜˜˜˜
imageProcessing.c:283:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
for(j = y - 3.5; j <= y + 3.5; j++) {
˜ ˜˜^˜˜˜˜
7 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 beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/beadarray.buildbin-libdir/beadarray/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (beadarray)
>>>>>>>
>>>>>>> FIXING LINKS FOR beadarray.buildbin-libdir/beadarray/libs//beadarray.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" "beadarray.buildbin-libdir/beadarray/libs//beadarray.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "beadarray.buildbin-libdir/beadarray/libs//beadarray.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" "beadarray.buildbin-libdir/beadarray/libs//beadarray.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "beadarray.buildbin-libdir/beadarray/libs//beadarray.so"