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Package 588/671HostnameOS / ArchBUILDCHECKBUILD BIN
SeqArray 1.0.0
Xiuwen Zheng
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/SeqArray
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: SeqArray
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SeqArray_1.0.0.tar.gz
StartedAt: 2013-05-01 10:48:24 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 10:49:18 -0700 (Wed, 01 May 2013)
EllapsedTime: 53.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SeqArray.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/SeqArray.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 'SeqArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqArray' 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 'SeqArray' can be installed ... [10s/13s] 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 compilation flags in Makevars ... 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 ... [13s/16s] OK
* 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

SeqArray.Rcheck/00install.out:

* installing *source* package 'SeqArray' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DCOREARRAY_NO_FORCEINLINE -DCOREARRAY_R_LINK -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c CoreGDSLink.cpp -o CoreGDSLink.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DCOREARRAY_NO_FORCEINLINE -DCOREARRAY_R_LINK -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c main.cpp -o main.o
main.cpp:148:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                return string(p, MaxNum) + "...";
                       ˜˜˜˜˜˜    ^˜˜˜˜˜
main.cpp:185:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if (s[i] == '/')
                    ˜ ^
main.cpp:187:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        s.insert(i+1, &prefix, 1);
                        ˜        ˜^˜
main.cpp:183:21: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        for (int i=s.size()-1; i >= 0; i--)
                 ˜ ˜˜˜˜˜˜˜˜^˜
main.cpp:236:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        TRUE_ARRAY.resize(Cnt, TRUE);
                        ˜˜˜˜˜˜˜˜˜˜        ^˜˜
main.cpp:367:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        _lines.resize(n);
                        ˜˜˜˜˜˜        ^
main.cpp:369:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                _lines[i] = CHAR(STRING_ELT(val, i));
                                ˜˜˜˜˜˜ ^
main.cpp:558:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                CHECK(gds_AppendString(data_obj, (*it)[j].c_str()));
                                                                                 ˜     ^
main.cpp:579:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        if (nMax < (int)I32ss[j].size())
                                                        ˜˜˜˜˜ ^
main.cpp:580:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                nMax = I32ss[j].size();
                                                       ˜˜˜˜˜ ^
main.cpp:582:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                I32s.resize(nTotalSample);
                                ˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:587:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                vector<CoreArray::Int32> &B = I32ss[j];
                                                                              ˜˜˜˜˜ ^
main.cpp:588:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                I32s[j] = (i < (int)B.size()) ? B[i] : NA_INTEGER;
                                                ˜˜˜˜ ^
main.cpp:588:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                I32s[j] = (i < (int)B.size()) ? B[i] : NA_INTEGER;
                                                                                ˜ ^
main.cpp:597:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        if (nMax < (int)F32ss[j].size())
                                                        ˜˜˜˜˜ ^
main.cpp:598:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                nMax = F32ss[j].size();
                                                       ˜˜˜˜˜ ^
main.cpp:600:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                F32s.resize(nTotalSample);
                                ˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:605:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                vector<float> &B = F32ss[j];
                                                                   ˜˜˜˜˜ ^
main.cpp:606:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                F32s[j] = (i < (int)B.size()) ? B[i] : (float)R_NaN;
                                                ˜˜˜˜ ^
main.cpp:606:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                F32s[j] = (i < (int)B.size()) ? B[i] : (float)R_NaN;
                                                                                ˜ ^
main.cpp:615:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        if (nMax < (int)UTF8ss[j].size())
                                                        ˜˜˜˜˜˜ ^
main.cpp:616:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                nMax = UTF8ss[j].size();
                                                       ˜˜˜˜˜˜ ^
main.cpp:622:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                vector<string> &B = UTF8ss[j];
                                                                    ˜˜˜˜˜˜ ^
main.cpp:624:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                        (i < (int)B.size()) ? B[i].c_str() : ""));
                                                                              ˜ ^
main.cpp:580:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                nMax = I32ss[j].size();
                                                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:598:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                nMax = F32ss[j].size();
                                                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:616:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                nMax = UTF8ss[j].size();
                                                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:665:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                out_len.resize(Cnt);
                ˜˜˜˜˜˜˜        ^˜˜
main.cpp:677:22: warning: implicit conversion changes signedness: 'CoreArray::Int32' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                out_var_sel.resize(out_var_count, TRUE);
                ˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:687:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if (sel[_start]) break;
                            ˜˜˜ ^˜˜˜˜˜
main.cpp:691:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if (sel[_end]) break;
                            ˜˜˜ ^˜˜˜
main.cpp:723:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        if (sel[pos+i])
                                            ˜˜˜ ˜˜˜^˜
main.cpp:661:12: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        int Cnt = CHECK(gds_SeqGetCount(Node));
            ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:689:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                int _end = sel.size()-1;
                    ˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:736:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                        out_var_count = out_var_sel.size();
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:894:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                Init.GENO_BUFFER.resize(CellCount);
                                ˜˜˜˜                    ^˜˜˜˜˜˜˜˜
main.cpp:965:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                Init.TRUE_ARRAY.resize(NumCellVariant);
                                ˜˜˜˜                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:975:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                vector<string> buffer(CellCount);
                                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main.cpp:978:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        SET_STRING_ELT(Val, i, mkChar(buffer[i].c_str()));
                                                                      ˜˜˜˜˜˜ ^
main.cpp:1205:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                vector<CBOOL> flag_array(Count);
                              ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1215:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                flag_array[i] = (base[i] == TRUE);
                                ˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1223:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        vector<int> sample_id(Count);
                                    ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1229:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                set<int>::iterator it = set_id.find(sample_id[i]);
                                                                    ˜˜˜˜˜˜˜˜˜ ^
main.cpp:1230:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                flag_array[i] = (it != set_id.end());
                                ˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1239:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        vector<double> sample_id(Count);
                                       ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1245:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                set<double>::iterator it = set_id.find(sample_id[i]);
                                                                       ˜˜˜˜˜˜˜˜˜ ^
main.cpp:1246:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                flag_array[i] = (it != set_id.end());
                                ˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1256:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        vector<string> sample_id(Count);
                                       ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1262:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                set<string>::iterator it = set_id.find(sample_id[i]);
                                                                       ˜˜˜˜˜˜˜˜˜ ^
main.cpp:1263:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                flag_array[i] = (it != set_id.end());
                                ˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1310:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                vector<CBOOL> flag_array(Count);
                              ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1320:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                flag_array[i] = (base[i] == TRUE);
                                ˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1328:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        vector<int> var_id(Count);
                                    ˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1334:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                set<int>::iterator it = set_id.find(var_id[i]);
                                                                    ˜˜˜˜˜˜ ^
main.cpp:1335:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                flag_array[i] = (it != set_id.end());
                                ˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1344:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        vector<double> variant_id(Count);
                                       ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1350:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                set<double>::iterator it = set_id.find(variant_id[i]);
                                                                       ˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1351:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                flag_array[i] = (it != set_id.end());
                                ˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1361:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        vector<string> variant_id(Count);
                                       ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1367:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                set<string>::iterator it = set_id.find(variant_id[i]);
                                                                       ˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1368:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                flag_array[i] = (it != set_id.end());
                                ˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1437:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        vector<int> split(Num_Process);
                    ˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
main.cpp:1443:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                split[i] = (int)(start + 0.5);
                ˜˜˜˜˜ ^
main.cpp:1451:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                CLEAR_SEL_VALUE(split[i] - st, it);
                                ˜˜˜˜˜ ^
main.cpp:1452:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                st = split[i];
                     ˜˜˜˜˜ ^
main.cpp:1454:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int ans_n = split[Process_Index] - st;
                    ˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1456:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        st = split[Process_Index];
             ˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1459:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                CLEAR_SEL_VALUE(split[i] - st, it);
                                ˜˜˜˜˜ ^
main.cpp:1460:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                st = split[i];
                     ˜˜˜˜˜ ^
main.cpp:1492:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        vector<int> split(Num_Process);
                    ˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
main.cpp:1498:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                split[i] = (int)(start + 0.5);
                ˜˜˜˜˜ ^
main.cpp:1506:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                CLEAR_SEL_VALUE(split[i] - st, it);
                                ˜˜˜˜˜ ^
main.cpp:1507:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                st = split[i];
                     ˜˜˜˜˜ ^
main.cpp:1509:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int ans_n = split[Process_Index] - st;
                    ˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1511:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        st = split[Process_Index];
             ˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1514:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                CLEAR_SEL_VALUE(split[i] - st, it);
                                ˜˜˜˜˜ ^
main.cpp:1515:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                st = split[i];
                     ˜˜˜˜˜ ^
main.cpp:1552:30: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                        PROTECT(tmp = NEW_LOGICAL(s.Sample.size()));
                                      ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:71:44: note: expanded from macro 'NEW_LOGICAL'
#define NEW_LOGICAL(n)          allocVector(LGLSXP,n)
                                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
main.cpp:1555:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                LOGICAL(tmp)[i] = (s.Sample[i] != 0);
                                                   ˜        ^
main.cpp:1566:30: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                        PROTECT(tmp = NEW_LOGICAL(s.Variant.size()));
                                      ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:71:44: note: expanded from macro 'NEW_LOGICAL'
#define NEW_LOGICAL(n)          allocVector(LGLSXP,n)
                                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
main.cpp:1569:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                LOGICAL(tmp)[i] = (s.Variant[i] != 0);
                                                   ˜         ^
main.cpp:1547:12: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                        int L = CHECK(gds_SeqGetCount(varSample));
                            ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1561:12: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                        int L = CHECK(gds_SeqGetCount(varVariant));
                            ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1617:23: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                                INTEGER(I32)[1] = gds_SeqGetCount(vSample);
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1618:23: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                                INTEGER(I32)[2] = gds_SeqGetCount(vVariant);
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1802:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        Sel.Variant.resize(DLen[0], TRUE);
                                        ˜˜˜                ^˜˜˜˜˜˜
main.cpp:1807:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        Sel.Sample.resize(DLen[1], TRUE);
                                        ˜˜˜               ^˜˜˜˜˜˜
main.cpp:1834:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                Sel.Sample.resize(Cnt, TRUE);
                                ˜˜˜               ^˜˜
main.cpp:1841:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                Sel.Variant.resize(Cnt, TRUE);
                                ˜˜˜                ^˜˜
main.cpp:1935:33: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                                                PROTECT(I32 = NEW_INTEGER(len.size()));
                                                              ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:72:44: note: expanded from macro 'NEW_INTEGER'
#define NEW_INTEGER(n)          allocVector(INTSXP,n)
                                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
main.cpp:1938:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                        base[i] = len[i];
                                                                  ˜˜˜ ^
main.cpp:1977:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                Sel.Sample.resize(DLen[1], TRUE);
                                ˜˜˜               ^˜˜˜˜˜˜
main.cpp:1979:24: warning: implicit conversion changes signedness: 'Int64' (aka 'long long') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                Sel.Variant.resize(gds_SeqGetCount(N_idx), TRUE);
                                ˜˜˜                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1995:31: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                                PROTECT(I32 = NEW_INTEGER(len.size()));
                                              ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:72:44: note: expanded from macro 'NEW_INTEGER'
#define NEW_INTEGER(n)          allocVector(INTSXP,n)
                                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
main.cpp:1998:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        base[i] = len[i];
                                                  ˜˜˜ ^
main.cpp:1832:15: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                                int Cnt = gds_SeqGetCount(N);
                                    ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1839:15: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                                int Cnt = gds_SeqGetCount(N);
                                    ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1856:29: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                        "genotype/data", Root, Sel.Variant.size(),
                                                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1857:23: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                        &Sel.Variant[0], Sel.Sample.size(), &Sel.Sample[0]);
                                                         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2053:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        Sel.Sample.resize(Cnt, TRUE);
                        ˜˜˜               ^˜˜
main.cpp:2060:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        Sel.Variant.resize(Cnt, TRUE);
                        ˜˜˜                ^˜˜
main.cpp:2079:45: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                vector<TVariable_ApplyByVariant> NodeList(Rf_length(var_name));
                                                 ˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2122:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        NodeList[i].InitObject(VarType, s.c_str(), Root, Sel.Variant.size(),
                        ˜˜˜˜˜˜˜˜ ^
main.cpp:2176:36: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                        PROTECT(R_call_param = NEW_LIST(NodeList.size()));
                                               ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:76:41: note: expanded from macro 'NEW_LIST'
#define NEW_LIST(n)             allocVector(VECSXP,n)
                                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
main.cpp:2051:14: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                        int Cnt = gds_SeqGetCount(N);
                            ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2058:14: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                        int Cnt = gds_SeqGetCount(N);
                            ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2122:53: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        NodeList[i].InitObject(VarType, s.c_str(), Root, Sel.Variant.size(),
                        ˜˜˜˜˜˜˜˜                                         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2123:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                &Sel.Variant[0], Sel.Sample.size(), &Sel.Sample[0]);
                                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2638:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n > 0) txt.append(s, n); else txt.push_back('.');
                   ˜˜˜           ^
main.cpp:2679:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        int L = _VCF4_INFO_Number[i];
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:2702:52: warning: implicit conversion changes signedness: 'unsigned long' to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                const char *nm = CHAR(STRING_ELT(VarNames, i + 8 + _VCF4_INFO_Number.size()));
                                      ˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:395:25: note: expanded from macro 'CHAR'
#define CHAR(x)         R_CHAR(x)
                               ^
main.cpp:2702:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                const char *nm = CHAR(STRING_ELT(VarNames, i + 8 + _VCF4_INFO_Number.size()));
                                                           ˜˜^˜˜ ˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:395:25: note: expanded from macro 'CHAR'
#define CHAR(x)         R_CHAR(x)
                               ^
main.cpp:2703:32: warning: implicit conversion changes signedness: 'unsigned long' to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SEXP D = VECTOR_ELT(X, i + 8 + _VCF4_INFO_Number.size());
                         ˜˜˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2703:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                SEXP D = VECTOR_ELT(X, i + 8 + _VCF4_INFO_Number.size());
                                       ˜˜^˜˜ ˜
main.cpp:2764:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        int L = _VCF4_FORMAT_Number[it->second];
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
main.cpp:2801:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (p != st) val.erase(0, p - st);
                     ˜˜˜          ˜˜^˜˜˜
main.cpp:2810:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        val.resize(L);
        ˜˜˜        ^
main.cpp:2803:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int L = val.size();
            ˜   ^˜˜˜˜˜˜˜˜˜
main.cpp:2840:9: warning: implicit conversion loses integer precision: 'long' to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
        return val;
        ˜˜˜˜˜˜ ^˜˜
main.cpp:2868:17: warning: implicit conversion loses integer precision: 'long' to 'const value_type' (aka 'const int') [-Wshorten-64-to-32]
                I32.push_back(val);
                ˜˜˜           ^˜˜
main.cpp:2885:9: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                val = R_NaN;
                    ˜ ^˜˜˜˜
main.cpp:2890:10: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                        val = R_NaN;
                            ˜ ^˜˜˜˜
main.cpp:2911:10: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                        val = R_NaN;
                            ˜ ^˜˜˜˜
main.cpp:3074:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                format_list.back().I32ss.resize(nTotalSamp);
                                                ˜˜˜˜˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜
main.cpp:3077:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                format_list.back().F32ss.resize(nTotalSamp);
                                                ˜˜˜˜˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜
main.cpp:3080:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                format_list.back().UTF8ss.resize(nTotalSamp);
                                                ˜˜˜˜˜˜˜˜˜˜˜                      ^˜˜˜˜˜˜˜˜˜
main.cpp:3102:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                I32s.reserve(nTotalSamp);
                ˜˜˜˜         ^˜˜˜˜˜˜˜˜˜
main.cpp:3106:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                F32s.reserve(nTotalSamp);
                ˜˜˜˜         ^˜˜˜˜˜˜˜˜˜
main.cpp:3110:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                StrList.reserve(nTotalSamp);
                ˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜˜˜
main.cpp:3114:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                Geno.resize(nTotalSamp);
                ˜˜˜˜        ^˜˜˜˜˜˜˜˜˜
main.cpp:3116:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                I8s.reserve(nTotalSamp * num_ploidy);
                ˜˜˜         ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3278:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                        CHECK(gds_AppendString(pInfo->data_obj, StrList[k].c_str()));
                                                                                                ˜˜˜˜˜˜˜ ^
main.cpp:3382:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                vector<Int16> &pAllele = Geno[samp_idx];
                                                         ˜˜˜˜ ^˜˜˜˜˜˜˜
main.cpp:3411:24: warning: implicit conversion loses integer precision: 'CoreArray::Int32' (aka 'int') to 'const value_type' (aka 'const short') [-Wconversion]
                                        pAllele.push_back(val);
                                        ˜˜˜˜˜˜˜           ^˜˜
main.cpp:3425:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        pAllele.resize(num_ploidy, -1);
                                        ˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜
main.cpp:3429:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        I32s.resize(num_ploidy-1, 0);
                                        ˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3435:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        CHECK(gds_AppendData(varPhaseExtra, Len, &(I32s[num_ploidy-1]), svInt32));
                                                                                   ˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3448:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        TVCF_Field_Format *pFmt = fmt_ptr[i];
                                                                  ˜˜˜˜˜˜˜ ^
main.cpp:3460:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                getInt32Array(value, pFmt->I32ss[samp_idx], RaiseError);
                                                                     ˜˜˜˜        ^˜˜˜˜˜˜˜
main.cpp:3461:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                pFmt->Check(pFmt->I32ss[samp_idx], name, num_allele, NA_INTEGER);
                                                            ˜˜˜˜        ^˜˜˜˜˜˜˜
main.cpp:3465:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                getFloatArray(value, pFmt->F32ss[samp_idx], RaiseError);
                                                                     ˜˜˜˜        ^˜˜˜˜˜˜˜
main.cpp:3466:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                pFmt->Check(pFmt->F32ss[samp_idx], name, num_allele, (float)R_NaN);
                                                            ˜˜˜˜        ^˜˜˜˜˜˜˜
main.cpp:3470:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                getStringArray(value, pFmt->UTF8ss[samp_idx]);
                                                                      ˜˜˜˜         ^˜˜˜˜˜˜˜
main.cpp:3471:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                pFmt->Check(pFmt->UTF8ss[samp_idx], name, num_allele, BlackString);
                                                            ˜˜˜˜         ^˜˜˜˜˜˜˜
main.cpp:3497:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        vector<Int16> &pAllele = Geno[i];
                                                                 ˜˜˜˜ ^
main.cpp:3499:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                I8s.push_back((pAllele[j] >> bits) & 0x03);
                                                               ˜˜˜˜˜˜˜ ^
main.cpp:3507:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                vector<Int16> &pGeno = Geno[i];
                                                       ˜˜˜˜ ^
main.cpp:3512:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        CHECK(gds_AppendData(varGenoExtra, Len, &(pGeno[num_ploidy-1]), svInt32));
                                                                                  ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3550:34: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                PROTECT(rv_ans = NEW_CHARACTER(filter_list.size()));
                                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:74:45: note: expanded from macro 'NEW_CHARACTER'
#define NEW_CHARACTER(n)        allocVector(STRSXP,n)
                                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
main.cpp:3552:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        SET_STRING_ELT(rv_ans, i, mkChar(filter_list[i].c_str()));
                                                         ˜˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:3219:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                        I32 = filter_list.size();
                                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3221:36: warning: implicit conversion loses integer precision: 'long' to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                        I32 = p - filter_list.begin() + 1;
                                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
main.cpp:3255:45: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                CHECK(gds_AppendData(pInfo->data_obj, I32s.size(), &(I32s[0]), svInt32));
                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜˜˜˜˜˜
main.cpp:3261:45: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                CHECK(gds_AppendData(pInfo->data_obj, F32s.size(), &(F32s[0]), svFloat32));
                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜˜˜˜˜˜
main.cpp:3389:29: warning: implicit conversion loses integer precision: 'long' to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                        CoreArray::Int32 val = strtol(p, &endptr, 10);
                                                         ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:413:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                I32 = array.size();
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3254:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Check<int>' requested here
                                                pInfo->Check(I32s, name, num_allele);
                                                       ^
main.cpp:418:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                I32 = array.size();
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:428:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                I32 = array.size();
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:413:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                I32 = array.size();
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3260:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Check<float>' requested here
                                                pInfo->Check(F32s, name, num_allele);
                                                       ^
main.cpp:418:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                I32 = array.size();
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:428:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                I32 = array.size();
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:413:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                I32 = array.size();
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3276:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Check<std::basic_string<char> >' requested here
                                                pInfo->Check(StrList, name, num_allele);
                                                       ^
main.cpp:418:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                I32 = array.size();
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:428:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
                                I32 = array.size();
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:457:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        array.resize(number, val);
                        ˜˜˜˜˜        ^˜˜˜˜˜
main.cpp:3297:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Fill<int>' requested here
                                                pInfo->Fill(I32s, NA_INTEGER);
                                                       ^
main.cpp:457:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        array.resize(number, val);
                        ˜˜˜˜˜        ^˜˜˜˜˜
main.cpp:3300:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Fill<float>' requested here
                                                pInfo->Fill(F32s, (float)R_NaN);
                                                       ^
main.cpp:457:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        array.resize(number, val);
                        ˜˜˜˜˜        ^˜˜˜˜˜
main.cpp:3307:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Fill<std::basic_string<char> >' requested here
                                                pInfo->Fill(StrList, string());
                                                       ^
main.cpp:501:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        array.resize(num_allele-1, missing);
                                        ˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3461:13: note: in instantiation of function template specialization 'TVCF_Field_Format::Check<int>' requested here
                                                pFmt->Check(pFmt->I32ss[samp_idx], name, num_allele, NA_INTEGER);
                                                      ^
main.cpp:512:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        array.resize((num_allele+1)*num_allele/2, missing);
                                        ˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:524:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                array.resize(number, missing);
                                                ˜˜˜˜˜        ^˜˜˜˜˜
main.cpp:501:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        array.resize(num_allele-1, missing);
                                        ˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3466:13: note: in instantiation of function template specialization 'TVCF_Field_Format::Check<float>' requested here
                                                pFmt->Check(pFmt->F32ss[samp_idx], name, num_allele, (float)R_NaN);
                                                      ^
main.cpp:512:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        array.resize((num_allele+1)*num_allele/2, missing);
                                        ˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:524:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                array.resize(number, missing);
                                                ˜˜˜˜˜        ^˜˜˜˜˜
main.cpp:501:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        array.resize(num_allele-1, missing);
                                        ˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3471:13: note: in instantiation of function template specialization 'TVCF_Field_Format::Check<std::basic_string<char> >' requested here
                                                pFmt->Check(pFmt->UTF8ss[samp_idx], name, num_allele, BlackString);
                                                      ^
main.cpp:512:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        array.resize((num_allele+1)*num_allele/2, missing);
                                        ˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:524:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                array.resize(number, missing);
                                                ˜˜˜˜˜        ^˜˜˜˜˜
176 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 SeqArray.so CoreGDSLink.o main.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/SeqArray.Rcheck/SeqArray/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 (SeqArray)

SeqArray.Rcheck/SeqArray-Ex.timings:

nameusersystemelapsed
SeqArray-package1.9130.0733.277
seqApply0.2100.0160.226
seqClose0.0510.0050.057
seqCompress.Option2.9260.0603.224
seqDelete1.5060.0301.553
seqExampleFileName0.0140.0030.016
seqGDS2VCF1.0530.0201.083
seqGetData0.0890.0110.109
seqGetFilter0.0700.0070.077
seqOpen0.0500.0050.056
seqParallel0.2620.0191.508
seqSetFilter0.0670.0080.078
seqSummary0.0600.0060.065
seqTranspose1.5940.0321.641
seqVCF.Header0.0480.0030.051
seqVCF.SampID0.0130.0030.016
seqVCF2GDS1.4620.0241.510