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INSTALL report for ChemmineR on tokay1

This page was generated on 2020-08-06 11:51:29 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChemmineR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 264/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 3.41.0
Thomas Girke
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/ChemmineR
Branch: master
Last Commit: d62c204
Last Changed Date: 2020-04-27 14:18:14 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  ERROR  skipped 
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] ERROR  skipped  skipped 
merida1 macOS 10.14.6 Mojave / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: ChemmineR
Version: 3.41.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ChemmineR_3.41.0.tar.gz && rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChemmineR.buildbin-libdir ChemmineR_3.41.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ChemmineR_3.41.0.zip && rm ChemmineR_3.41.0.tar.gz ChemmineR_3.41.0.zip
StartedAt: 2020-08-05 17:07:30 -0400 (Wed, 05 Aug 2020)
EndedAt: 2020-08-05 17:11:34 -0400 (Wed, 05 Aug 2020)
EllapsedTime: 244.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ChemmineR_3.41.0.tar.gz && rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChemmineR.buildbin-libdir ChemmineR_3.41.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ChemmineR_3.41.0.zip && rm ChemmineR_3.41.0.tar.gz ChemmineR_3.41.0.zip
###
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##############################################################################


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100  780k  100  780k    0     0  18.1M      0 --:--:-- --:--:-- --:--:-- 20.0M

install for i386

* installing *source* package 'ChemmineR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DisjointSets.cpp -o DisjointSets.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cluster.cc -o cluster.o
cluster.cc: In function 'int nbr_intersect(std::vector<int>&, std::vector<int>&)':
cluster.cc:118:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
         ~~^~~~~~~~~~~~~~
cluster.cc:118:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
                              ~~^~~~~~~~~~~~~~
cluster.cc: In function 'int contains(int, std::vector<int>&)':
cluster.cc:131:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i=0; i < list.size(); i++)
               ~~^~~~~~~~~~~~~
cluster.cc: In function 'DisjointSets cluster(int, int, int, int)':
cluster.cc:267:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (int j = 0; j < nbr_list[i].size(); j ++) {
                   ~~^~~~~~~~~~~~~~~~~~~~
cluster.cc: In function 'void loadNNMatrix(int, int, int, SEXP)':
cluster.cc:284:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                    ~^~
cluster.cc:298:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(nbrs.size() < minNbrs) // will end up a singleton
      ~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function 'void loadNNList(int, int, SEXP)':
cluster.cc:314:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                    ~^~
cluster.cc:332:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(nbrs.size() < minNbrs) // will end up a singleton
      ~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function 'SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)':
cluster.cc:390:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  for(unsigned i=0; i<N; i++){
                    ~^~
cluster.cc: At global scope:
cluster.cc:49:13: warning: 'void prepare_neighbors(const char*, int, int)' defined but not used [-Wunused-function]
 void static prepare_neighbors(const char* nbr_file, int skip, int p)
             ^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cstrsplit.cc -o cstrsplit.o
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/as_literal.hpp:22,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cstrsplit.cc:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c desc.cc -o desc.o
desc.cc: In function 'SEXPREC* genAPDescriptor(SEXP)':
desc.cc:249:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<unsigned int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i=0; i < descs.size(); i++)
               ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function 'SEXPREC* uniquifyAtomPairs(SEXP)':
fingerprints.cc:138:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i=0; i < aps.size(); i++)
               ~~^~~~~~~~~~~~
fingerprints.cc:145:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
               ~~^~~~~~~~~~~~
fingerprints.cc:158:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
               ~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c formats.cc -o formats.o
formats.cc: In function 'int sdf_iter(std::fstream&, std::__cxx11::string&, int&)':
formats.cc:237:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation]
   strncpy(buf_4, line, 4);
   ~~~~~~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c molecule.cc -o molecule.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c r_wrap.cc -o r_wrap.o
r_wrap.cc: In function 'SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)':
r_wrap.cc:949:15: warning: variable 'p' set but not used [-Wunused-but-set-variable]
   const char *p = typeName;
               ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c script.cc -o script.o
In file included from script.cc:2:
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
 static char elements[112][3] = {
             ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c similarity.cc -o similarity.o
In file included from similarity.cc:1:
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
 static char elements[112][3] = {
             ^~~~~~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChemmineR.dll tmp.def DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ChemmineR.buildbin-libdir/00LOCK-ChemmineR/00new/ChemmineR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ChemmineR'
    finding HTML links ... done
    AP-class                                html  
    APset-class                             html  
    ExtSDF-class                            html  
    FP-class                                html  
    FPset-class                             html  
    SDF-class                               html  
    SDF2apcmp                               html  
    SDFDataTable                            html  
    SDFset-class                            html  
    SDFset2SDF                              html  
    SDFset2list                             html  
    SDFstr-class                            html  
    SMI-class                               html  
    SMIset-class                            html  
    addDescriptorType                       html  
    addNewFeatures                          html  
    ap                                      html  
    apfp                                    html  
    apset                                   html  
    apset2descdb                            html  
    atomblock                               html  
    atomcount                               html  
    atomprop                                html  
    atomsubset                              html  
    batchByIndex                            html  
    bondblock                               html  
    bonds                                   html  
    browseJob                               html  
    bufferLines                             html  
    bufferResultSet                         html  
    byCluster                               html  
    canonicalNumbering                      html  
    canonicalize                            html  
    cid                                     html  
    cluster.sizestat                        html  
    cluster.visualize                       html  
    cmp.cluster                             html  
    cmp.duplicated                          html  
    cmp.parse                               html  
    cmp.parse1                              html  
    cmp.search                              html  
    cmp.similarity                          html  
    conMA                                   html  
    connections                             html  
    datablock                               html  
    datablock2ma                            html  
    db.explain                              html  
    db.subset                               html  
    dbTransaction                           html  
    desc2fp                                 html  
    draw_sdf                                html  
    exactMassOB                             html  
    findCompounds                           html  
    findCompoundsByName                     html  
    fingerprintOB                           html  
    fold                                    html  
    foldCount                               html  
    fp2bit                                  html  
    fpSim                                   html  
    fptype                                  html  
    fromNNMatrix                            html  
    genAPDescriptors                        html  
    genParameters                           html  
    generate3DCoords                        html  
    getAllCompoundIds                       html  
    getCompoundFeatures                     html  
    getCompoundNames                        html  
    getCompounds                            html  
    getIds                                  html  
    grepSDFset                              html  
    groups                                  html  
    header                                  html  
    initDb                                  html  
    jarvisPatrick                           html  
    jarvisPatrick_c                         html  
    jobToken-class                          html  
    largestComponent                        html  
    launchCMTool                            html  
    listCMTools                             html  
    listFeatures                            html  
    loadSdf                                 html  
    makeUnique                              html  
    maximallyDissimilar                     html  
    nearestNeighbors                        html  
    numBits                                 html  
    obmol                                   html  
    openBabelPlot                           html  
    parBatchByIndex                         html  
    plotStruc                               html  
    propOB                                  html  
    pubchemCidToSDF                         html  
    pubchemFPencoding                       html  
    pubchemName2CID                         html  
    pubchemSDFSearch                        html  
    pubchemSmilesSearch                     html  
    read.AP                                 html  
    read.SDFindex                           html  
    read.SDFset                             html  
    read.SDFstr                             html  
    read.SMIset                             html  
    regenerateCoords                        html  
    result                                  html  
    rings                                   html  
    sdf.subset                              html  
    sdf.visualize                           html  
    sdf2ap                                  html  
    sdf2list                                html  
    sdf2smiles                              html  
    sdf2str                                 html  
    sdfStream                               html  
    sdfid                                   html  
    sdfsample                               html  
    sdfstr2list                             html  
    searchSim                               html  
    searchString                            html  
    selectInBatches                         html  
    setPriorities                           html  
    smartsSearchOB                          html  
    smiles2sdf                              html  
    smisample                               html  
    status                                  html  
    toolDetails                             html  
    trimNeighbors                           html  
    validSDF                                html  
    view                                    html  
    write.SDF                               html  
    write.SDFsplit                          html  
    write.SMI                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ChemmineR' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DisjointSets.cpp -o DisjointSets.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cluster.cc -o cluster.o
cluster.cc: In function 'int nbr_intersect(std::vector<int>&, std::vector<int>&)':
cluster.cc:118:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
         ~~^~~~~~~~~~~~~~
cluster.cc:118:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
                              ~~^~~~~~~~~~~~~~
cluster.cc: In function 'int contains(int, std::vector<int>&)':
cluster.cc:131:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0; i < list.size(); i++)
               ~~^~~~~~~~~~~~~
cluster.cc: In function 'DisjointSets cluster(int, int, int, int)':
cluster.cc:267:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (int j = 0; j < nbr_list[i].size(); j ++) {
                   ~~^~~~~~~~~~~~~~~~~~~~
cluster.cc: In function 'void loadNNMatrix(int, int, int, SEXP)':
cluster.cc:284:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                    ~^~
cluster.cc:298:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(nbrs.size() < minNbrs) // will end up a singleton
      ~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function 'void loadNNList(int, int, SEXP)':
cluster.cc:314:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                    ~^~
cluster.cc:332:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(nbrs.size() < minNbrs) // will end up a singleton
      ~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function 'SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)':
cluster.cc:390:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  for(unsigned i=0; i<N; i++){
                    ~^~
cluster.cc: At global scope:
cluster.cc:49:13: warning: 'void prepare_neighbors(const char*, int, int)' defined but not used [-Wunused-function]
 void static prepare_neighbors(const char* nbr_file, int skip, int p)
             ^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cstrsplit.cc -o cstrsplit.o
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/as_literal.hpp:22,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cstrsplit.cc:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c desc.cc -o desc.o
desc.cc: In function 'SEXPREC* genAPDescriptor(SEXP)':
desc.cc:249:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0; i < descs.size(); i++)
               ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function 'SEXPREC* uniquifyAtomPairs(SEXP)':
fingerprints.cc:138:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0; i < aps.size(); i++)
               ~~^~~~~~~~~~~~
fingerprints.cc:145:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
               ~~^~~~~~~~~~~~
fingerprints.cc:158:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
               ~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c formats.cc -o formats.o
formats.cc: In function 'int sdf_iter(std::fstream&, std::__cxx11::string&, int&)':
formats.cc:237:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation]
   strncpy(buf_4, line, 4);
   ~~~~~~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c molecule.cc -o molecule.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c r_wrap.cc -o r_wrap.o
r_wrap.cc: In function 'SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)':
r_wrap.cc:949:15: warning: variable 'p' set but not used [-Wunused-but-set-variable]
   const char *p = typeName;
               ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c script.cc -o script.o
In file included from script.cc:2:
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
 static char elements[112][3] = {
             ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c similarity.cc -o similarity.o
In file included from similarity.cc:1:
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
 static char elements[112][3] = {
             ^~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChemmineR.dll tmp.def DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChemmineR' as ChemmineR_3.41.0.zip
* DONE (ChemmineR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ChemmineR' successfully unpacked and MD5 sums checked