ASEB 1.4.0
Likun Wang
| 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/ASEB | | 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=ASEB.buildbin-libdir ASEB_1.4.0.tar.gz'
>>>>>>>
* installing *source* package 'ASEB' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c asebC.cpp -o asebC.o
asebC.cpp:295:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(sequence[i] == 'K'){
˜˜˜˜˜˜˜˜ ^
asebC.cpp:296:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
string site_seq = sequence.substr(i-8, 17);
˜˜˜˜˜˜˜˜ ˜^˜
asebC.cpp:311:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(sequence[i] == 'K'){
˜˜˜˜˜˜˜˜ ^
asebC.cpp:312:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
string site_seq = sequence.substr(i-8, 17);
˜˜˜˜˜˜˜˜ ˜^˜
asebC.cpp:329:78: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int score = get_score_seqs(id2seq[protein_name], id2seq[total_poteins[i]]);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:330:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
score_matrix.push_back(pair<string, int>(total_poteins[i], score));
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:346:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(score_matrix[i].second > 0){
˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:347:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
score_matrix[i].second = score_matrix[i].second/max_pos;
˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:347:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
score_matrix[i].second = score_matrix[i].second/max_pos;
˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:349:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(score_matrix[i].second < 0){
˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:350:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
score_matrix[i].second = score_matrix[i].second/min_neg;
˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:350:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
score_matrix[i].second = score_matrix[i].second/min_neg;
˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:352:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
geneName2rank[score_matrix[i].first] = i;
˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:368:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
indexes.reserve(size);
˜˜˜˜˜˜˜ ^˜˜˜
asebC.cpp:365:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int max = score_matrix.size();
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:366:15: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int size = predefined.size();
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:400:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
random_index.push_back(geneName2rank[total_poteins[rand_num2]]);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
asebC.cpp:390:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int max = total_poteins.size();
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:424:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rand_str[i] = str1[indexes[i]];
˜˜˜˜˜˜˜˜ ^
asebC.cpp:424:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rand_str[i] = str1[indexes[i]];
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:424:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rand_str[i] = str1[indexes[i]];
˜˜˜˜˜˜˜ ^
asebC.cpp:428:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rand_str[i] = str1[indexes[i-1]];
˜˜˜˜˜˜˜˜ ^
asebC.cpp:428:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rand_str[i] = str1[indexes[i-1]];
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:428:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rand_str[i] = str1[indexes[i-1]];
˜˜˜˜˜˜˜ ˜^˜
asebC.cpp:414:15: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int size = str1.size();
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
asebC.cpp:540:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
char chr1 = str1[i];
˜˜˜˜ ^
asebC.cpp:541:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
char chr2 = str2[i];
˜˜˜˜ ^
asebC.cpp:569:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(score_matrix[indexes[i]].second > 0){
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:569:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(score_matrix[indexes[i]].second > 0){
˜˜˜˜˜˜˜ ^
asebC.cpp:570:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Nr+=score_matrix[indexes[i]].second;
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:570:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Nr+=score_matrix[indexes[i]].second;
˜˜˜˜˜˜˜ ^
asebC.cpp:572:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Nr-=score_matrix[indexes[i]].second;
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:572:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Nr-=score_matrix[indexes[i]].second;
˜˜˜˜˜˜˜ ^
asebC.cpp:575:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ES_current = (score_matrix[indexes[0]].second/Nr)-(double)indexes[0]/(N-Nh);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:581:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:581:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
˜˜˜˜˜˜˜ ^
asebC.cpp:581:77: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
˜˜˜˜˜˜˜ ^
asebC.cpp:581:89: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
˜˜˜˜˜˜˜ ˜^˜
asebC.cpp:565:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int N = score_matrix.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:597:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(score_matrix[indexes[i]].second > 0){
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:597:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(score_matrix[indexes[i]].second > 0){
˜˜˜˜˜˜˜ ^
asebC.cpp:598:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Nr+=score_matrix[indexes[i]].second;
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:598:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Nr+=score_matrix[indexes[i]].second;
˜˜˜˜˜˜˜ ^
asebC.cpp:600:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Nr-=score_matrix[indexes[i]].second;
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:600:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Nr-=score_matrix[indexes[i]].second;
˜˜˜˜˜˜˜ ^
asebC.cpp:605:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ES_current = (score_matrix[indexes[0]].second/Nr)-(double)indexes[0]/(N-Nh);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:607:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
line2 += double2str(ES_current-score_matrix[indexes[0]].second/Nr)+"\t";
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:615:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:615:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
˜˜˜˜˜˜˜ ^
asebC.cpp:615:77: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
˜˜˜˜˜˜˜ ^
asebC.cpp:615:89: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
˜˜˜˜˜˜˜ ˜^˜
asebC.cpp:620:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
line1 += int2str(indexes[i])+"\t";
˜˜˜˜˜˜˜ ^
asebC.cpp:621:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
line2 += double2str(ES_current-score_matrix[indexes[i]].second/Nr)+"\t";
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:621:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
line2 += double2str(ES_current-score_matrix[indexes[i]].second/Nr)+"\t";
˜˜˜˜˜˜˜ ^
asebC.cpp:622:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
line1 += int2str(indexes[i]+1)+"\t";
˜˜˜˜˜˜˜ ^
asebC.cpp:593:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int N = score_matrix.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:625:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
line1 += int2str(score_matrix.size())+"\t";
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:634:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(predefined.count(score_matrix[i].first) != 0){
˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:644:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(predefined.count(score_matrix[i].first) != 0){
˜˜˜˜˜˜˜˜˜˜˜˜ ^
59 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 ASEB.so asebC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ASEB.buildbin-libdir/ASEB/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 (ASEB)
>>>>>>>
>>>>>>> FIXING LINKS FOR ASEB.buildbin-libdir/ASEB/libs//ASEB.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" "ASEB.buildbin-libdir/ASEB/libs//ASEB.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "ASEB.buildbin-libdir/ASEB/libs//ASEB.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" "ASEB.buildbin-libdir/ASEB/libs//ASEB.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "ASEB.buildbin-libdir/ASEB/libs//ASEB.so"