triplex 1.0.7
Jiri Hon
| 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/triplex | | Last Changed Rev: 76143 / Revision: 76155 | | Last Changed Date: 2013-04-30 03:04:31 -0700 (Tue, 30 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=triplex.buildbin-libdir triplex_1.0.7.tar.gz'
>>>>>>>
* installing *source* package 'triplex' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_triplex.c -o R_init_triplex.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c align.c -o align.o
align.c:53:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
seq_l = strlen(seq);
˜ ^˜˜˜˜˜˜˜˜˜˜
align.c:136:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
body1[i1++] = toupper(nukl2char(seq[seq_l-1-row]));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align.c:137:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
body2[i2++] = toupper(nukl2char(seq[col]));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align.c:262:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
t_diag** mat = (t_diag**)malloc(size*sizeof(t_diag*));
^˜˜˜˜
align.c:270:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mat[x] = (t_diag*)malloc(size*sizeof(t_diag));
^˜˜˜˜
align.c:360:28: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
diag[d] = get_max_score(piece[i], piece[i-x], diag[d-1], diag[d], diag[d+1], d, x, params->tri_type, params->max_loop, pen);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
align.c:360:38: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
diag[d] = get_max_score(piece[i], piece[i-x], diag[d-1], diag[d], diag[d+1], d, x, params->tri_type, params->max_loop, pen);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c align_interface.c -o align_interface.o
align_interface.c:47:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.tri_type = t[0],
^˜˜˜
align_interface.c:48:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.min_score = p[P_MIN_SCORE],
^˜˜˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:50:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.min_len = p[P_MIN_LEN],
^˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:51:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.max_len = p[P_MAX_LEN],
^˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:52:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.min_loop = p[P_MIN_LOOP],
^˜˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:53:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.max_loop = p[P_MAX_LOOP],
^˜˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:58:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.dtwist = p[P_DTWIST_PEN],
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:62:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.mismatch = p[P_MIS_PEN]
^˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:59:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.insertion = p[P_INS_PEN],
^˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:60:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.iso_change = p[P_ISO_PEN],
^˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:61:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.iso_stay = p[P_ISO_BONUS],
^˜˜˜˜˜˜˜˜˜˜˜˜˜
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c dl_list.c -o dl_list.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c libtriplex.c -o libtriplex.o
libtriplex.c:262:7: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
ch = tolower(ch);
˜ ^˜˜˜˜˜˜˜˜˜˜
libtriplex.c:406:36: warning: implicit conversion changes signedness: 'int' to 'unsigned char' [-Wsign-conversion]
unsigned char i = 0, j = 0, max = - 99, tmp;
˜˜˜ ^˜˜˜
libtriplex.c:410:10: warning: implicit conversion loses integer precision: 'const int' to 'unsigned char' [-Wconversion]
tmp = tab_score[triplex_type][n1[i]][n2[j]];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
libtriplex.c:419:10: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
*a = n1[i];
˜ ^˜˜˜˜
libtriplex.c:420:10: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
*b = n2[j];
˜ ^˜˜˜˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c progress.c -o progress.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c search.c -o search.o
search.c:86:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
int pieces = ceil(chunk_l / (double) params.max_chunk_size);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
search.c:71:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int chunk_l = strlen(chunk);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
search.c:80:28: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int chunk_offset = chunk - dna.seq;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
search.c:101:29: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int piece_offset = piece - chunk;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜
search.c:283:28: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
diag[d] = get_max_score(piece[i], piece[i-x], diag[d-1], diag[d], diag[d+1], d, x, params->tri_type, params->max_loop, pen);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
search.c:283:38: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
diag[d] = get_max_score(piece[i], piece[i-x], diag[d-1], diag[d], diag[d+1], d, x, params->tri_type, params->max_loop, pen);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c search_interface.c -o search_interface.o
search_interface.c:50:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
dna.seq[i] = tolower(DNAdecode(x.seq[i]));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:218:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.min_score = p[P_MIN_SCORE],
^˜˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:220:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.min_len = p[P_MIN_LEN],
^˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:221:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.max_len = p[P_MAX_LEN],
^˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:222:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.min_loop = p[P_MIN_LOOP],
^˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:223:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.max_loop = p[P_MAX_LOOP],
^˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:229:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.dtwist = p[P_DTWIST_PEN],
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:233:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.mismatch = p[P_MIS_PEN]
^˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:230:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.insertion = p[P_INS_PEN],
^˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:231:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.iso_change = p[P_ISO_PEN],
^˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:232:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
.iso_stay = p[P_ISO_BONUS],
^˜˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:246:45: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
dl_list_init(&dl_list_arr[i], p[P_MAX_LEN]+p[P_MAX_LOOP]); // FIXME
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
12 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 triplex.so Biostrings_stubs.o IRanges_stubs.o R_init_triplex.o align.o align_interface.o dl_list.o libtriplex.o progress.o search.o search_interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/triplex.buildbin-libdir/triplex/libs
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (triplex)
>>>>>>>
>>>>>>> FIXING LINKS FOR triplex.buildbin-libdir/triplex/libs//triplex.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" "triplex.buildbin-libdir/triplex/libs//triplex.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "triplex.buildbin-libdir/triplex/libs//triplex.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" "triplex.buildbin-libdir/triplex/libs//triplex.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "triplex.buildbin-libdir/triplex/libs//triplex.so"