BioC 2.12: CHECK report for ExpressionView on pelham

Package: ExpressionView

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ExpressionView_1.12.0.tar.gz

StartedAt: 2013-05-01 05:06:47 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:11:18 -0700 (Wed, 01 May 2013)

EllapsedTime: 270.8 seconds

RetCode: 0

Status: OK

CheckDir: ExpressionView.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ExpressionView.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 'ExpressionView/DESCRIPTION' ... OK
* this is package 'ExpressionView' version '1.12.0'
* 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 'ExpressionView' can be installed ... [26s/27s] 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 ... NOTE
NB: .Last.lib will not be used unless it is exported
* 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' ... NOTE
The following directories should probably not be installed:
  'figures'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [54s/56s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
ExportEV 31.034  2.101  34.712
OrderEV   9.926  1.096  11.166
* 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/ExpressionView.Rcheck/00check.log'
for details.

* installing *source* package 'ExpressionView' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c order.cpp -o order.o
order.cpp:53:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        order.resize(nrows);
        ˜˜˜˜˜        ^˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1049:17: note: expanded from macro 'nrows'
#define nrows                   Rf_nrows
                                ^˜˜˜˜˜˜˜
order.cpp:56:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        data.resize(nrows);
        ˜˜˜˜        ^˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1049:17: note: expanded from macro 'nrows'
#define nrows                   Rf_nrows
                                ^˜˜˜˜˜˜˜
order.cpp:59:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                order[row] = INTEGER(_order)[row] - 1;
                ˜˜˜˜˜ ^˜˜
order.cpp:60:8: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                data[row].resize(ncolumns);
                ˜˜˜˜ ^˜˜
order.cpp:60:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                data[row].resize(ncolumns);
                ˜˜˜˜             ^˜˜˜˜˜˜˜
order.cpp:63:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        data[row][column] = temp;
                        ˜˜˜˜ ^˜˜
order.cpp:63:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        data[row][column] = temp;
                        ˜˜˜˜      ^˜˜˜˜˜
order.cpp:103:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                INTEGER(result)[row] = clusters.order[row] + 1;
                                       ˜˜˜˜˜˜˜˜       ^˜˜
order.cpp:125:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  cres = R_alloc(nlen+1, sizeof(char));
         ˜˜˜˜˜˜˜ ˜˜˜˜^˜
order.cpp:128:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    memcpy(pt, p, pos);
    ˜˜˜˜˜˜        ^˜˜
order.cpp:134:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    memcpy(pt, p, rem);
    ˜˜˜˜˜˜        ^˜˜
order.cpp:116:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int slen=strlen(str);
      ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
12 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c orderclusters.cpp -o orderclusters.o
orderclusters.cpp:54:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        order.resize(nSlots);
        ˜˜˜˜˜        ^˜˜˜˜˜
orderclusters.cpp:56:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                order[slot] = _order[slot];
                ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:56:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                order[slot] = _order[slot];
                              ˜˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:59:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        multiplicity.resize(nSlots, 1);
        ˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜
orderclusters.cpp:60:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        optimallength.resize(nClusters);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜
orderclusters.cpp:63:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                maximalcluster[i].resize(nClusters);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
orderclusters.cpp:63:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                maximalcluster[i].resize(nClusters);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜
orderclusters.cpp:51:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        nSlots = data.size();
               ˜ ^˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:52:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        nClusters = data[0].size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:67:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
orderclusters.cpp:78:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        data.resize(nSlots);
        ˜˜˜˜        ^˜˜˜˜˜
orderclusters.cpp:80:8: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                data[slot].resize(nClusters, 0);
                ˜˜˜˜ ^˜˜˜
orderclusters.cpp:80:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                data[slot].resize(nClusters, 0);
                ˜˜˜˜              ^˜˜˜˜˜˜˜˜
orderclusters.cpp:83:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        order.resize(nSlots);
        ˜˜˜˜˜        ^˜˜˜˜˜
orderclusters.cpp:85:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                order[slot] = slot;
                ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:88:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        multiplicity.resize(nSlots, 1);
        ˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜
orderclusters.cpp:89:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        optimallength.resize(nClusters);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜
orderclusters.cpp:92:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                maximalcluster[i].resize(nClusters);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
orderclusters.cpp:92:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                maximalcluster[i].resize(nClusters);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜
orderclusters.cpp:108:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        data[slot][cluster] = 1;
                        ˜˜˜˜ ^˜˜˜
orderclusters.cpp:108:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        data[slot][cluster] = 1;
                        ˜˜˜˜       ^˜˜˜˜˜˜
orderclusters.cpp:110:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                optimallength[cluster] = right - left + 1;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
orderclusters.cpp:127:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                data[slot][cluster] = 1;
                                ˜˜˜˜ ^˜˜˜
orderclusters.cpp:127:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                data[slot][cluster] = 1;
                                ˜˜˜˜       ^˜˜˜˜˜˜
orderclusters.cpp:134:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
orderclusters.cpp:159:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[slot1] == data[slot2] ) {
                             ˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:159:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[slot1] == data[slot2] ) {
                                            ˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:165:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if ( accumulate(data[slot1].begin(), data[slot1].end(), 0) == 0 ) {
                                ˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:165:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if ( accumulate(data[slot1].begin(), data[slot1].end(), 0) == 0 ) {
                                                     ˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:170:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        newdata.push_back(data[slot1]);
                                          ˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:187:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if ( discard.find(order[slot]) == discard.end() ) {
                                  ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:188:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        neworder.push_back(temporder[order[slot]]);
                                                     ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:199:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        length += data[slot][cluster];
                                  ˜˜˜˜ ^˜˜˜
orderclusters.cpp:199:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        length += data[slot][cluster];
                                  ˜˜˜˜       ^˜˜˜˜˜˜
orderclusters.cpp:201:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                optimallength[cluster] = length;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
orderclusters.cpp:172:58: warning: implicit conversion loses integer precision: 'unsigned long' to 'const int' [-Wshorten-64-to-32]
                        temporder.insert ( pair<int, int>(slot1,newdata.size()-1) );
                                           ˜˜˜˜                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
orderclusters.cpp:194:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        nSlots = data.size();
               ˜ ^˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:220:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for ( set<int>::iterator slotp = redundantslots[order[slot]].begin(); slotp != redundantslots[order[slot]].end(); slotp++ ) {
                                                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:220:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for ( set<int>::iterator slotp = redundantslots[order[slot]].begin(); slotp != redundantslots[order[slot]].end(); slotp++ ) {
                                                                ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:220:97: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for ( set<int>::iterator slotp = redundantslots[order[slot]].begin(); slotp != redundantslots[order[slot]].end(); slotp++ ) {
                                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:220:103: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for ( set<int>::iterator slotp = redundantslots[order[slot]].begin(); slotp != redundantslots[order[slot]].end(); slotp++ ) {
                                                                                                              ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:225:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for ( set<int>::iterator slotp = redundantslots[nSlots].begin(); slotp != redundantslots[nSlots].end(); slotp++ ) {
                                                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
orderclusters.cpp:225:92: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for ( set<int>::iterator slotp = redundantslots[nSlots].begin(); slotp != redundantslots[nSlots].end(); slotp++ ) {
                                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
orderclusters.cpp:238:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        multiplicity.resize(nSlots, 1);
        ˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜
orderclusters.cpp:230:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        nSlots = neworder.size();
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:255:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                int temp = order[slot1];
                           ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:256:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                order[slot1] = order[slot2];
                ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:256:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                order[slot1] = order[slot2];
                               ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:257:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                order[slot2] = temp;
                ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:251:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int slot1 = order.size();
            ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:321:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double result = inner_product(data[order[slot1]].begin(), data[order[slot1]].end(), data[order[slot2]].begin(), 0.);
                                      ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:321:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double result = inner_product(data[order[slot1]].begin(), data[order[slot1]].end(), data[order[slot2]].begin(), 0.);
                                           ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:321:65: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double result = inner_product(data[order[slot1]].begin(), data[order[slot1]].end(), data[order[slot2]].begin(), 0.);
                                                                  ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:321:71: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double result = inner_product(data[order[slot1]].begin(), data[order[slot1]].end(), data[order[slot2]].begin(), 0.);
                                                                       ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:321:91: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double result = inner_product(data[order[slot1]].begin(), data[order[slot1]].end(), data[order[slot2]].begin(), 0.);
                                                                                            ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:321:97: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double result = inner_product(data[order[slot1]].begin(), data[order[slot1]].end(), data[order[slot2]].begin(), 0.);
                                                                                                 ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:330:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        int l1 = maximalcluster[1][cluster];
                                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜
orderclusters.cpp:331:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        int l2 = maximalcluster[2][cluster];
                                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜
orderclusters.cpp:376:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[order[slot]][*cluster] ) {
                             ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:376:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[order[slot]][*cluster] ) {
                                  ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:376:27: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[order[slot]][*cluster] ) {
                             ˜˜˜˜              ^˜˜˜˜˜˜˜
orderclusters.cpp:377:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                length += multiplicity[order[slot]];
                                          ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:377:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                length += multiplicity[order[slot]];
                                                       ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:400:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                maximalcluster[0][*cluster] = maxlength;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜˜
orderclusters.cpp:401:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                maximalcluster[1][*cluster] = maxl1;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜˜
orderclusters.cpp:402:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                maximalcluster[2][*cluster] = maxl2;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜˜
orderclusters.cpp:422:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        optimum += data[slot][cluster] * multiplicity[slot];
                                   ˜˜˜˜ ^˜˜˜
orderclusters.cpp:422:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        optimum += data[slot][cluster] * multiplicity[slot];
                                   ˜˜˜˜       ^˜˜˜˜˜˜
orderclusters.cpp:422:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        optimum += data[slot][cluster] * multiplicity[slot];
                                                         ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:433:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int temp = order[slot1];
                   ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:434:8: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        order[slot1] = order[slot2];
        ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:434:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        order[slot1] = order[slot2];
                       ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:435:8: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        order[slot2] = temp;
        ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:452:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        neworder.push_back(order[slot]);
                                           ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:455:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        neworder.push_back(order[slot]);
                                           ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:459:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        neworder.push_back(order[slot]);
                                           ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:462:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        neworder.push_back(order[slot]);
                                           ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:468:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                order[slot] = neworder[slotp++];
                ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:468:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                order[slot] = neworder[slotp++];
                              ˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜
orderclusters.cpp:526:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[order[start]][cluster] ) {
                             ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:526:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[order[start]][cluster] ) {
                                  ˜˜˜˜˜ ^˜˜˜˜
orderclusters.cpp:526:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[order[start]][cluster] ) {
                             ˜˜˜˜               ^˜˜˜˜˜˜
orderclusters.cpp:531:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                if ( !data[order[end]][cluster] ) {
                                      ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
orderclusters.cpp:531:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                if ( !data[order[end]][cluster] ) {
                                           ˜˜˜˜˜ ^˜˜
orderclusters.cpp:531:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                if ( !data[order[end]][cluster] ) {
                                      ˜˜˜˜             ^˜˜˜˜˜˜
orderclusters.cpp:583:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int maxlength = ( what ) ? optimallength[cluster] : nSlots - optimallength[cluster];
                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
orderclusters.cpp:583:77: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int maxlength = ( what ) ? optimallength[cluster] : nSlots - optimallength[cluster];
                                                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
orderclusters.cpp:590:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[order[slot]][cluster] ) {
                             ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:590:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[order[slot]][cluster] ) {
                                  ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:590:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( data[order[slot]][cluster] ) {
                             ˜˜˜˜              ^˜˜˜˜˜˜
orderclusters.cpp:594:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( !data[order[slot]][cluster] ) {
                              ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:594:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( !data[order[slot]][cluster] ) {
                                   ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:594:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( !data[order[slot]][cluster] ) {
                              ˜˜˜˜              ^˜˜˜˜˜˜
orderclusters.cpp:601:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        permutation.resize(nslots);
        ˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜
orderclusters.cpp:603:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                permutation[i] = i;
                ˜˜˜˜˜˜˜˜˜˜˜ ^
orderclusters.cpp:622:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                swapslots.push_back(make_pair(slot,order[slot]));
                                                                   ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:630:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                print("%d ", swapslots[i].first);
                                             ˜˜˜˜˜˜˜˜˜ ^
orderclusters.cpp:638:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                order[swapslots[slot].first] = swapslots[permutation[slot]].second;
                                ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
orderclusters.cpp:638:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                order[swapslots[slot].first] = swapslots[permutation[slot]].second;
                                      ˜˜˜˜˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:638:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                order[swapslots[slot].first] = swapslots[permutation[slot]].second;
                                                               ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:638:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                order[swapslots[slot].first] = swapslots[permutation[slot]].second;
                                                                         ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:650:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        order[swapslots[slot].first] = swapslots[bestpermutation[slot]].second;
                        ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
orderclusters.cpp:650:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        order[swapslots[slot].first] = swapslots[bestpermutation[slot]].second;
                              ˜˜˜˜˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:650:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        order[swapslots[slot].first] = swapslots[bestpermutation[slot]].second;
                                                       ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:650:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        order[swapslots[slot].first] = swapslots[bestpermutation[slot]].second;
                                                                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:619:45: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                        int slot = random(0, possibleslots.size()-1);
                                   ˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
orderclusters.cpp:755:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                print("%3d %3d %3d: ", slot, order[slot], multiplicity[order[slot]]);
                                             ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:755:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                print("%3d %3d %3d: ", slot, order[slot], multiplicity[order[slot]]);
                                                          ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:755:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                print("%3d %3d %3d: ", slot, order[slot], multiplicity[order[slot]]);
                                                                       ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:757:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        print("%d", data[order[slot]][cluster]);
                                    ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
orderclusters.cpp:757:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        print("%d", data[order[slot]][cluster]);
                                         ˜˜˜˜˜ ^˜˜˜
orderclusters.cpp:757:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        print("%d", data[order[slot]][cluster]);
                                    ˜˜˜˜              ^˜˜˜˜˜˜
112 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 ExpressionView.so order.o orderclusters.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ExpressionView.Rcheck/ExpressionView/libs
** R
** inst
** preparing package for lazy loading
in method for 'ExportEV' with signature 'biclusters="Biclust"': no definition for class "Biclust"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ExpressionView)

name	user	system	elapsed
ExportEV	31.034	2.101	34.712
LaunchEV	0.002	0.004	0.007
OrderEV	9.926	1.096	11.166

Summary

Command output