cisPath 1.0.0
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/cisPath | | 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=cisPath.buildbin-libdir cisPath_1.0.0.tar.gz'
>>>>>>>
* installing *source* package 'cisPath' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c cisPath.cpp -o cisPath.o
cisPath.cpp:50:31: warning: implicit conversion changes signedness: 'const char' to 'unsigned long' [-Wsign-conversion]
__h = 107 * __h + str[i];
˜ ^˜˜˜˜˜
cisPath.cpp:304:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
addLink(current, onePath[index + 1], -1, 1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
cisPath.cpp:311:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(current == onePath[index + 1])
˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
cisPath.cpp:316:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
current = onePath[index + 1];
˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
cisPath.cpp:363:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
getPath(tokens[i]);
˜˜˜˜˜˜ ^
cisPath.cpp:388:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(targets.count(hasPath[i]) != 0)
˜˜˜˜˜˜˜ ^
cisPath.cpp:390:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
example = hasPath[i];
˜˜˜˜˜˜˜ ^
cisPath.cpp:416:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((targetFile != "") && (targets.count(hasPath[i]) == 0))
˜˜˜˜˜˜˜ ^
cisPath.cpp:425:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
string pName = hasPath[i];
˜˜˜˜˜˜˜ ^
cisPath.cpp:430:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pName = pName + "," + hasPath[i];
˜˜˜˜˜˜˜ ^
cisPath.cpp:433:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
OUTJSALL << "\"" << hasPath[i] << "\":1";
˜˜˜˜˜˜˜ ^
cisPath.cpp:437:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
string jsFile = outputDir + "/js/" + hasPath[i] + "_path.js";
˜˜˜˜˜˜˜ ^
cisPath.cpp:444:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
jsFile = outputDir + "/js/" + hasPath[i] + "_graph.js";
˜˜˜˜˜˜˜ ^
cisPath.cpp:453:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
getPath(hasPath[i]);
˜˜˜˜˜˜˜ ^
cisPath.cpp:476:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
OUTJSALL << "\"" << OutPutID2names[i] << "\"";
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:498:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
VALIDOUT << validInputs[i] << "\n";
˜˜˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:513:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
dist[nodes[i]] = INF;
˜˜˜˜˜ ^
cisPath.cpp:514:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
prev[nodes[i]] = nodes[i];
˜˜˜˜˜ ^
cisPath.cpp:514:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
prev[nodes[i]] = nodes[i];
˜˜˜˜˜ ^
cisPath.cpp:516:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tmp.name = nodes[i];
˜˜˜˜˜ ^
cisPath.cpp:518:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(nodes[i] == root)
˜˜˜˜˜ ^
cisPath.cpp:521:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
dist[nodes[i]] = 0;
˜˜˜˜˜ ^
cisPath.cpp:538:15: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int ccc = u.size();
˜˜˜ ^˜˜˜˜˜˜˜
cisPath.cpp:542:19: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int ccc = s.size();
˜˜˜ ^˜˜˜˜˜˜˜
cisPath.cpp:626:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
ccc = s.size();
˜ ^˜˜˜˜˜˜˜
cisPath.cpp:739:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((pubmedIds[index].substr(0, 7) == "pubmed:") &&
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
cisPath.cpp:740:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(pubmedIds[index].substr(0, 17) != "pubmed:unassigned"))
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
cisPath.cpp:744:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pubmedstr = pubmedIds[index].substr(7);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
cisPath.cpp:749:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
string id = pubmedIds[index].substr(7);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
cisPath.cpp:926:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pubmedstr = pubmedIds[index];
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
cisPath.cpp:931:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
string id = pubmedIds[index];
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
cisPath.cpp:1017:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
string_tokenize(edgeInfo[currentNode + "&" + m1], ", ").size();
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cisPath.cpp:1019:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
string_tokenize(edgeInfo[currentNode + "&" + m2], ", ").size();
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cisPath.cpp:1121:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(edgeInfo.count(allChilds[i] + "&" + mainNodes[j]) != 0)
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1121:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(edgeInfo.count(allChilds[i] + "&" + mainNodes[j]) != 0)
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1123:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
valideNodes.push_back(mainNodes[j]);
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1134:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
addLink(valideNodes[j], allChilds[i], changeint(i) + 1000, -1);
˜˜˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1134:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
addLink(valideNodes[j], allChilds[i], changeint(i) + 1000, -1);
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1153:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(edgeInfo.count(allChilds[i] + "&" + mainNodes[j]) != 0)
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1153:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(edgeInfo.count(allChilds[i] + "&" + mainNodes[j]) != 0)
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1155:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
valideNodes.push_back(mainNodes[j]);
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1166:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
addLink(valideNodes[j], allChilds[i], 7 + 1000, -1);
˜˜˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1166:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
addLink(valideNodes[j], allChilds[i], 7 + 1000, -1);
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1548:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
string aChild = allChilds[i];
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1552:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(edgeInfo.count(allChilds[i] + "&" + mainNodes[j]) != 0)
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1552:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(edgeInfo.count(allChilds[i] + "&" + mainNodes[j]) != 0)
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1554:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
valideNodes.push_back(mainNodes[j]);
˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1582:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
addColorLink(valideNodes[j], aChild);
˜˜˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1689:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
addColorNodeStr(proteinNodes[i]);
˜˜˜˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1690:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
string name = proteinNodes[i];
˜˜˜˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1701:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
string source = proteinNodes[i];
˜˜˜˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1702:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
string target = proteinNodes[j];
˜˜˜˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1772:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((tokens[i][0] == ' ') || (tokens[i][0] == '{'))
˜˜˜˜˜˜ ^
cisPath.cpp:1772:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((tokens[i][0] == ' ') || (tokens[i][0] == '{'))
˜˜˜˜˜˜ ^
cisPath.cpp:1774:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tokens[i] = tokens[i].substr(1);
˜˜˜˜˜˜ ^
cisPath.cpp:1774:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tokens[i] = tokens[i].substr(1);
˜˜˜˜˜˜ ^
cisPath.cpp:1778:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tokens[i] = tokens[i].substr(0, tokens[i].size() - 2);
˜˜˜˜˜˜ ^
cisPath.cpp:1778:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tokens[i] = tokens[i].substr(0, tokens[i].size() - 2);
˜˜˜˜˜˜ ^
cisPath.cpp:1778:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tokens[i] = tokens[i].substr(0, tokens[i].size() - 2);
˜˜˜˜˜˜ ^
cisPath.cpp:1780:65: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<string> smalltokens = string_tokenize(tokens[i], ":", false);
˜˜˜˜˜˜ ^
cisPath.cpp:1785:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
name += (":" + smalltokens[i]);
˜˜˜˜˜˜˜˜˜˜˜ ^
cisPath.cpp:1823:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
OUTJSALL << lines[i] << "\n";
˜˜˜˜˜ ^
62 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 cisPath.so cisPath.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/cisPath.buildbin-libdir/cisPath/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 (cisPath)
>>>>>>>
>>>>>>> FIXING LINKS FOR cisPath.buildbin-libdir/cisPath/libs//cisPath.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" "cisPath.buildbin-libdir/cisPath/libs//cisPath.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "cisPath.buildbin-libdir/cisPath/libs//cisPath.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" "cisPath.buildbin-libdir/cisPath/libs//cisPath.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "cisPath.buildbin-libdir/cisPath/libs//cisPath.so"