##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChemmineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ChemmineR_3.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ChemmineR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChemmineR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineR' version '3.40.0'
* 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 whether package 'ChemmineR' can be installed ... WARNING
Found the following significant warnings:
  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]
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ChemmineR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'png' 'ChemmineOB'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'ChemmineDrugs' 'ChemmineOB' 'RPostgreSQL' 'RSQLite' 'fmcsR' 'png'
  'snow'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'BiocGenerics'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'ChemmineR/R/sim.R':
  unlockBinding(".progress_bar_int_cnt", environment(.progress_bar))

.data.frame.to.str: no visible global function definition for
  'write.table'
.data.frame.to.str: no visible binding for global variable 'string'
.parseV3000: no visible binding for global variable 'AW'
.rings: no visible global function definition for 'combn'
DUD: no visible global function definition for 'download.file'
DUD: no visible global function definition for 'untar'
applyOptions: no visible global function definition for 'convertFormat'
browseJob: no visible global function definition for 'browseURL'
canonicalNumbering: no visible global function definition for
  'canonicalNumbering_OB'
canonicalNumberingOB: no visible global function definition for
  'canonicalNumbering_OB'
cluster.visualize: no visible global function definition for 'rainbow'
cluster.visualize: no visible global function definition for 'pdf'
cluster.visualize: no visible global function definition for
  'postscript'
cluster.visualize: no visible global function definition for 'dev.off'
desc2fp: no visible global function definition for 'data'
draw_sdf: no visible global function definition for 'rgb'
draw_sdf: no visible global function definition for 'fmcs'
exactMassOB: no visible global function definition for 'exactMass_OB'
fingerprintOB: no visible global function definition for
  'fingerprint_OB'
getCompoundFeatures : <anonymous>: no visible global function
  definition for 'write.table'
getCompounds: no visible global function definition for 'str'
getDbConn: no visible global function definition for 'error'
handle_segs: no visible binding for global variable 'C1'
handle_segs: no visible binding for global variable 'C2'
handle_segs: no visible binding for global variable 'C1.1'
handle_segs: no visible binding for global variable 'C2.1'
handle_text: no visible binding for global variable 'C1'
handle_text: no visible binding for global variable 'C2'
listCMTools: no visible global function definition for 'read.table'
parBatchByIndex: no visible global function definition for
  'clusterExport'
parBatchByIndex: no visible global function definition for
  'clusterApplyLB'
postgresqlWriteTable: no visible global function definition for
  'postgresqlTableRef'
postgresqlWriteTable: no visible global function definition for
  'postgresqlQuoteId'
postgresqlWriteTable: no visible global function definition for
  'postgresqlpqExec'
postgresqlWriteTable: no visible global function definition for
  'postgresqlCopyInDataframe'
postgresqlWriteTable: no visible global function definition for
  'postgresqlgetResult'
propOB: no visible global function definition for 'prop_OB'
read.AP: no visible global function definition for 'read.delim'
sdf2OBMol: no visible global function definition for 'forEachMol'
sdf2image: no visible global function definition for 'convertToImage'
sdf2smiles: no visible global function definition for 'convertFormat'
sdf2smilesOB: no visible global function definition for 'convertFormat'
sdfStream: no visible global function definition for 'write.table'
setPriorities: no visible global function definition for
  'clusterExport'
smartsSearchOB: no visible global function definition for
  'smartsSearch_OB'
smile2sdfFile: no visible global function definition for
  'convertFormatFile'
smiles2sdf: no visible global function definition for 'convertFormat'
smiles2sdfOB: no visible global function definition for 'convertFormat'
write.SMI: no visible global function definition for 'write.table'
Undefined global functions or variables:
  AW C1 C1.1 C2 C2.1 browseURL canonicalNumbering_OB clusterApplyLB
  clusterExport combn convertFormat convertFormatFile convertToImage
  data dev.off download.file error exactMass_OB fingerprint_OB fmcs
  forEachMol pdf postgresqlCopyInDataframe postgresqlQuoteId
  postgresqlTableRef postgresqlgetResult postgresqlpqExec postscript
  prop_OB rainbow read.delim read.table rgb smartsSearch_OB str string
  untar write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "postscript", "rainbow",
             "rgb")
  importFrom("utils", "browseURL", "combn", "data", "download.file",
             "read.delim", "read.table", "str", "untar", "write.table")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/ChemmineR/libs/i386/ChemmineR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/ChemmineR/libs/x64/ChemmineR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
SDFDataTable 1.81   0.11    14.7
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
       test_ea.comparison 
       test_ea.dupDescriptors 
  
     test_general.R 
       test.3dCoords 
       test.genAPDescriptors 
       test.largestComponent 
       test.parseV3000 
       test.propOB 
       test.pubchemPUG 
  
  
  Error in BiocGenerics:::testPackage("ChemmineR") : 
    unit tests failed for package ChemmineR
  Execution halted
** running tests for arch 'x64' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
       test.parseV3000 
       test.propOB 
       test.pubchemPUG 
  
  
  Error in BiocGenerics:::testPackage("ChemmineR") : 
    unit tests failed for package ChemmineR
  In addition: Warning messages:
  1: In for (i in seq_along(methods)) { :
    closing unused connection 5 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/smiles/C1CCCCCC1/SDF)
  2: In for (i in seq_along(methods)) { :
    closing unused connection 4 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/434,435/SDF)
  3: In for (i in seq_along(testData)) { :
    closing unused connection 3 (C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpIN3xBA\file10281fd04cf0)
  Execution halted
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/ChemmineR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ChemmineR_3.40.0.tar.gz && rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChemmineR.buildbin-libdir ChemmineR_3.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ChemmineR_3.40.0.zip && rm ChemmineR_3.40.0.tar.gz ChemmineR_3.40.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 14  777k   14  112k    0     0   485k      0  0:00:01 --:--:--  0:00:01  497k
100  777k  100  777k    0     0  2636k      0 --:--:-- --:--:-- --:--:-- 2689k

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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/as_literal.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.11-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-3.11-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-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/as_literal.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.11-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-3.11-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-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChemmineR' as ChemmineR_3.40.0.zip
* DONE (ChemmineR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ChemmineR' successfully unpacked and MD5 sums checked