Thomas Girke
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/ChemmineR |
| git_branch: RELEASE_3_13 |
| git_last_commit: 6a834ab |
| git_last_commit_date: 2021-05-19 11:42:00 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the ChemmineR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChemmineR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 285/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChemmineR 3.44.0 (landing page) Thomas Girke
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: ChemmineR |
| Version: 3.44.0 |
| Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ChemmineR_3.44.0.tar.gz && rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChemmineR.buildbin-libdir ChemmineR_3.44.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ChemmineR_3.44.0.zip && rm ChemmineR_3.44.0.tar.gz ChemmineR_3.44.0.zip |
| StartedAt: 2021-10-14 08:25:36 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 08:27:09 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 93.3 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ChemmineR_3.44.0.tar.gz && rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChemmineR.buildbin-libdir ChemmineR_3.44.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ChemmineR_3.44.0.zip && rm ChemmineR_3.44.0.tar.gz ChemmineR_3.44.0.zip
###
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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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChemmineR' as ChemmineR_3.44.0.zip
* DONE (ChemmineR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ChemmineR' successfully unpacked and MD5 sums checked