TargetSearch 1.16.0
Alvaro Cuadros-Inostroza
| 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/TargetSearch | | 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=TargetSearch.buildbin-libdir TargetSearch_1.16.0.tar.gz'
>>>>>>>
* installing *source* package 'TargetSearch' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c file.c -o file.o
file.c:72:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.ri = (double *) R_alloc(splen, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:73:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.rt = (double *) R_alloc(splen, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:74:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.n = (int *) R_alloc(splen, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:75:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.pk = (struct peaks *) R_alloc(splen, sizeof(struct peaks));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:77:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
fread(spectra.ri, splen * sizeof(double), 1, fp);
^˜˜˜˜ ˜
file.c:78:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
fread(spectra.rt, splen * sizeof(double), 1, fp);
^˜˜˜˜ ˜
file.c:79:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
fread(spectra.n, splen * sizeof(int), 1, fp);
^˜˜˜˜ ˜
file.c:87:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.pk[0].mass = (int *) R_alloc(sptotal, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
file.c:88:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.pk[0].in = (int *) R_alloc(sptotal, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
file.c:95:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
fread(spectra.pk[i].mass, spectra.n[i] * sizeof(int), 1, fp);
^˜˜˜˜˜˜˜˜˜˜˜ ˜
file.c:96:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
fread(spectra.pk[i].in, spectra.n[i] * sizeof(int), 1, fp);
^˜˜˜˜˜˜˜˜˜˜˜ ˜
file.c:187:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.ri = (double *) R_alloc(total, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:188:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.rt = (double *) R_alloc(total, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:189:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.n = (int *) R_alloc(total, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:190:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.pk = (struct peaks *) R_alloc(total, sizeof(struct peaks));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:209:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
str_alloc(ri_str, ri_len, len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./file.h:14:52: note: expanded from macro 'str_alloc'
x = (char *) R_chk_calloc(len, sizeof(char)); \
^
file.c:210:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
str_alloc(rt_str, rt_len, len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./file.h:14:52: note: expanded from macro 'str_alloc'
x = (char *) R_chk_calloc(len, sizeof(char)); \
^
file.c:211:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
str_alloc(sp_str, sp_len, len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./file.h:14:52: note: expanded from macro 'str_alloc'
x = (char *) R_chk_calloc(len, sizeof(char)); \
^
file.c:243:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.pk[j].mass = (int *) R_alloc(n , sizeof(int));
˜˜˜˜˜˜˜ ^
file.c:244:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
spectra.pk[j].in = (int *) R_alloc(n , sizeof(int));
˜˜˜˜˜˜˜ ^
file.c:275:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
sp_len = strlen(spectrum);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
file.c:350:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sp.ri = (double *) R_alloc(splen, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:351:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sp.rt = (double *) R_alloc(splen, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:352:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sp.n = (int *) R_alloc(splen, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:353:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sp.pk = (struct peaks *) R_alloc(splen, sizeof(struct peaks));
˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:354:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sp.pk[0].mass = (int *) R_alloc(sptotal, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
file.c:355:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sp.pk[0].in = (int *) R_alloc(sptotal, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
27 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c find_peaks.c -o find_peaks.o
find_peaks.c:117:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
b = ri[0];
˜ ^˜˜˜˜
find_peaks.c:120:26: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
i = (ri_min - b) / m;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
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 getLine.c -o getLine.o
getLine.c:11:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
*line = (char *) R_chk_calloc(*n, sizeof(char));
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
getLine.c:19:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
*line = (char *) R_chk_realloc(*line, *n * sizeof(char));
^˜ ˜
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 hpf.c -o hpf.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ncdf.c -o ncdf.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c netcdf_peak_finding.c -o netcdf_peak_finding.o
netcdf_peak_finding.c:60:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
diff = (int *) R_alloc( N * (scan_number - 1), sizeof(int));
˜˜˜˜˜˜˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
netcdf_peak_finding.c:61:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
x = (int *) R_alloc( N, sizeof(int));
˜˜˜˜˜˜˜ ^
netcdf_peak_finding.c:62:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
y = (int *) R_alloc( N, sizeof(int));
˜˜˜˜˜˜˜ ^
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 peakExtraction.c -o peakExtraction.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ppc.c -o ppc.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 TargetSearch.so Rinit.o file.o find_peaks.o getLine.o hpf.o ncdf.o netcdf_peak_finding.o peakExtraction.o ppc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/TargetSearch.buildbin-libdir/TargetSearch/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 (TargetSearch)
>>>>>>>
>>>>>>> FIXING LINKS FOR TargetSearch.buildbin-libdir/TargetSearch/libs//TargetSearch.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" "TargetSearch.buildbin-libdir/TargetSearch/libs//TargetSearch.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "TargetSearch.buildbin-libdir/TargetSearch/libs//TargetSearch.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" "TargetSearch.buildbin-libdir/TargetSearch/libs//TargetSearch.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "TargetSearch.buildbin-libdir/TargetSearch/libs//TargetSearch.so"