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Package 124/671HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: cisPath
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cisPath_1.0.0.tar.gz
StartedAt: 2013-05-01 03:48:52 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 03:50:31 -0700 (Wed, 01 May 2013)
EllapsedTime: 98.9 seconds
RetCode: 0
Status:  OK 
CheckDir: cisPath.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cisPath.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cisPath/DESCRIPTION' ... OK
* this is package 'cisPath' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'cisPath' can be installed ... [4s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [64s/69s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
cisPath         40.677  1.743  45.591
addProteinNames 18.955  0.956  21.918
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

cisPath.Rcheck/00install.out:

* installing *source* package 'cisPath' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -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.Rcheck/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)

cisPath.Rcheck/cisPath-Ex.timings:

nameusersystemelapsed
addProteinNames18.955 0.95621.918
cisPath40.677 1.74345.591
easyEditor0.0300.0100.041
networkView0.2510.0340.361