BioC 3.0: CHECK report for ChemmineR on moscato1

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ChemmineR.buildbin-libdir ChemmineR.Rcheck && mkdir ChemmineR.buildbin-libdir ChemmineR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChemmineR.buildbin-libdir ChemmineR_2.18.1.tar.gz >ChemmineR.Rcheck\00install.out 2>&1 && cp ChemmineR.Rcheck\00install.out ChemmineR-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ChemmineR.buildbin-libdir --install="check:ChemmineR-install.out" --force-multiarch --no-vignettes --timings ChemmineR_2.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ChemmineR.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '2.18.1'
* 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 ... OK
* 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:
  'methods' 'ChemmineOB' 'ChemmineDrugs'
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' '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 binding for global variable 'string'
applyOptions: no visible global function definition for 'convertFormat'
canonicalNumbering: no visible global function definition for
  'canonicalNumbering_OB'
canonicalNumberingOB: no visible global function definition for
  'canonicalNumbering_OB'
exactMassOB: no visible global function definition for 'exactMass_OB'
fingerprintOB: no visible global function definition for
  'fingerprint_OB'
getDbConn: no visible global function definition for 'error'
insertDef: no visible global function definition for
  'dbGetPreparedQuery'
insertDescriptor: no visible global function definition for
  'dbGetPreparedQuery'
insertDescriptorType: no visible global function definition for
  'dbGetPreparedQuery'
insertFeature: no visible global function definition for
  'dbGetPreparedQuery'
insertNamedDef: no visible global function definition for
  'dbGetPreparedQuery'
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'
sdf2OBMol: no visible global function definition for 'forEachMol'
sdf2smiles: no visible global function definition for 'convertFormat'
sdf2smilesOB: no visible global function definition for 'convertFormat'
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'
updatePriorities: no visible global function definition for
  'dbGetPreparedQuery'
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 'D:/biocbld/bbs-3.0-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/libs/i386/ChemmineR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/libs/x64/ChemmineR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [85s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
generate3DCoords 28.88      0   34.05
** running examples for arch 'x64' ... [80s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
generate3DCoords 24.79   0.02    25.3
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [59s]
 [59s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [49s]
 [49s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: 'RefManageR'
* 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

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/ChemmineR.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'ChemmineR' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c DisjointSets.cpp -o DisjointSets.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c cluster.cc -o cluster.o
cluster.cc: In function 'int nbr_intersect(std::vector<int>&, std::vector<int>&)':
cluster.cc:118:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc:118:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function 'int contains(int, std::vector<int>&)':
cluster.cc:131:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function 'DisjointSets cluster(int, int, int, int)':
cluster.cc:267:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function 'void loadNNMatrix(int, int, int, SEXP)':
cluster.cc:284:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc:298:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function 'void loadNNList(int, int, SEXP)':
cluster.cc:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc:332:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function 'SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)':
cluster.cc:390:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: At global scope:
cluster.cc:49:13: warning: 'void prepare_neighbors(const char*, int, int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c desc.cc -o desc.o
desc.cc: In function 'SEXPREC* genAPDescriptor(SEXP)':
desc.cc:249:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function 'SEXPREC* uniquifyAtomPairs(SEXP)':
fingerprints.cc:137:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
fingerprints.cc:144:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
fingerprints.cc:157:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c formats.cc -o formats.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c molecule.cc -o molecule.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c script.cc -o script.o
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c similarity.cc -o similarity.o
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
g++ -m32 -shared -s -static-libgcc -o ChemmineR.dll tmp.def DisjointSets.o cluster.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'as.vector' from package 'base' in package 'ChemmineR'
Creating a generic function for 'as.matrix' from package 'base' in package 'ChemmineR'
Creating a generic function for 'plot' from package 'graphics' in package 'ChemmineR'
Creating a generic function for 'print' from package 'base' in package 'ChemmineR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'ChemmineR' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c DisjointSets.cpp -o DisjointSets.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c cluster.cc -o cluster.o
cluster.cc: In function 'int nbr_intersect(std::vector<int>&, std::vector<int>&)':
cluster.cc:118:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc:118:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function 'int contains(int, std::vector<int>&)':
cluster.cc:131:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function 'DisjointSets cluster(int, int, int, int)':
cluster.cc:267:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function 'void loadNNMatrix(int, int, int, SEXP)':
cluster.cc:284:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc:298:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function 'void loadNNList(int, int, SEXP)':
cluster.cc:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc:332:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function 'SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)':
cluster.cc:390:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: At global scope:
cluster.cc:49:13: warning: 'void prepare_neighbors(const char*, int, int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c desc.cc -o desc.o
desc.cc: In function 'SEXPREC* genAPDescriptor(SEXP)':
desc.cc:249:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function 'SEXPREC* uniquifyAtomPairs(SEXP)':
fingerprints.cc:137:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
fingerprints.cc:144:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
fingerprints.cc:157:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c formats.cc -o formats.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c molecule.cc -o molecule.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c script.cc -o script.o
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=core2 -c similarity.cc -o similarity.o
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
g++ -m64 -shared -s -static-libgcc -o ChemmineR.dll tmp.def DisjointSets.o cluster.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChemmineR' as ChemmineR_2.18.1.zip
* DONE (ChemmineR)

name	user	system	elapsed
AP-class	0.50	0.04	0.55
APset-class	0.43	0.04	0.45
FP-class	0.14	0.00	0.14
FPset-class	0.48	0.00	0.49
SDF-class	0.07	0.00	0.07
SDF2apcmp	0.03	0.00	0.03
SDFset-class	0.44	0.01	0.45
SDFset2SDF	0.19	0.00	0.19
SDFset2list	0.11	0.00	0.11
SDFstr-class	0.54	0.00	0.55
SMI-class	0	0	0
SMIset-class	0.02	0.00	0.02
addDescriptorType	0	0	0
addNewFeatures	3.48	0.13	3.62
ap	0.11	0.00	0.10
apfp	0	0	0
apset	0	0	0
apset2descdb	0.39	0.04	0.44
atomblock	0.11	0.02	0.12
atomcount	0.23	0.03	0.26
atomprop	0	0	0
atomsubset	0.05	0.00	0.05
batchByIndex	0	0	0
bondblock	0.11	0.00	0.11
bonds	0.04	0.00	0.05
browseJob	0	0	0
bufferLines	0	0	0
bufferResultSet	0	0	0
byCluster	1.19	0.02	1.20
canonicalNumbering	0.42	0.00	4.19
canonicalize	0.07	0.00	0.17
cid	0.05	0.00	0.04
cluster.sizestat	0.85	0.00	0.86
cluster.visualize	0.86	0.00	0.86
cmp.cluster	3.42	0.00	3.41
cmp.duplicated	0.09	0.00	0.10
cmp.parse	0.03	0.00	0.03
cmp.parse1	0	0	0
cmp.search	0.89	0.01	0.90
cmp.similarity	0.02	0.00	0.01
conMA	0.08	0.00	0.08
connections	0.25	0.02	0.36
datablock	0.34	0.00	0.34
datablock2ma	0.05	0.00	0.05
db.explain	0.04	0.00	0.04
db.subset	0.02	0.00	0.02
dbTransaction	0.06	0.00	0.06
desc2fp	0.16	0.00	0.16
exactMassOB	0.98	0.01	1.95
findCompounds	2.60	0.00	2.61
findCompoundsByName	0.58	0.02	0.59
fingerprintOB	0	0	0
fold	0	0	0
foldCount	0	0	0
fp2bit	0.44	0.06	1.01
fpSim	0.47	0.02	0.49
fptype	0	0	0
fromNNMatrix	1.06	0.00	1.06
genAPDescriptors	0.01	0.00	0.02
generate3DCoords	28.88	0.00	34.05
getAllCompoundIds	0.42	0.00	0.42
getCompoundFeatures	0.47	0.01	0.49
getCompoundNames	0.48	0.00	0.48
getCompounds	0.53	0.00	0.53
getIds	0	0	0
grepSDFset	0.06	0.00	0.06
groups	0.14	0.00	0.14
header	0.11	0.00	0.11
initDb	0.05	0.00	0.05
jarvisPatrick	2.57	0.02	2.59
jobToken-class	0	0	0
launchCMTool	0	0	0
listCMTools	0	0	0
listFeatures	0.46	0.01	0.47
loadSdf	3.93	0.00	4.72
makeUnique	0.04	0.00	0.05
maximallyDissimilar	0.52	0.00	0.52
nearestNeighbors	1.71	0.00	1.71
numBits	0	0	0
obmol	0.05	0.00	0.05
parBatchByIndex	0	0	0
plotStruc	0.31	0.00	0.31
propOB	0	0	0
pubchemFPencoding	0.02	0.00	0.02
read.AP	0.01	0.00	0.01
read.SDFindex	0.02	0.00	0.02
read.SDFset	0.67	0.00	0.67
read.SDFstr	1	0	1
read.SMIset	0.01	0.00	0.02
regenerateCoords	0	0	0
result	0	0	0
rings	0.59	0.00	0.59
sdf.subset	0	0	0
sdf.visualize	0.02	0.00	0.02
sdf2ap	0.56	0.05	0.61
sdf2list	0.03	0.00	0.03
sdf2smiles	0	0	0
sdf2str	0.05	0.00	0.04
sdfStream	0.01	0.00	0.02
sdfid	0.04	0.00	0.03
sdfsample	0.06	0.00	0.06
sdfstr2list	1.65	0.16	1.81
searchSim	0	0	0
searchString	0	0	0
selectInBatches	0	0	0
setPriorities	0.02	0.00	0.02
smartsSearchOB	0	0	0
smiles2sdf	0	0	0
smisample	0	0	0
status	0	0	0
toolDetails	0	0	0
trimNeighbors	2.61	0.00	2.61
validSDF	0.01	0.01	0.03
view	0.07	0.00	0.06
write.SDF	0.2	0.0	0.2
write.SDFsplit	0.04	0.00	0.03
write.SMI	0	0	0

name	user	system	elapsed
AP-class	0.58	0.00	0.58
APset-class	0.45	0.00	0.45
FP-class	0.17	0.00	0.17
FPset-class	0.50	0.02	0.52
SDF-class	0.08	0.01	0.09
SDF2apcmp	0.08	0.00	0.08
SDFset-class	0.53	0.00	0.53
SDFset2SDF	0.14	0.02	0.16
SDFset2list	0.04	0.03	0.08
SDFstr-class	0.36	0.00	0.35
SMI-class	0.00	0.02	0.02
SMIset-class	0	0	0
addDescriptorType	0	0	0
addNewFeatures	3.44	0.09	3.67
ap	0.12	0.00	0.12
apfp	0.02	0.00	0.01
apset	0	0	0
apset2descdb	0.45	0.02	0.47
atomblock	0.14	0.00	0.14
atomcount	0.26	0.00	0.27
atomprop	0.02	0.00	0.01
atomsubset	0.01	0.01	0.03
batchByIndex	0	0	0
bondblock	0.15	0.00	0.14
bonds	0.03	0.00	0.03
browseJob	0	0	0
bufferLines	0	0	0
bufferResultSet	0	0	0
byCluster	1.16	0.00	1.15
canonicalNumbering	0.36	0.00	3.72
canonicalize	0.05	0.00	0.16
cid	0.03	0.00	0.03
cluster.sizestat	0.76	0.00	0.76
cluster.visualize	0.95	0.00	0.95
cmp.cluster	3.60	0.02	3.62
cmp.duplicated	0.10	0.00	0.09
cmp.parse	0.03	0.00	0.03
cmp.parse1	0	0	0
cmp.search	0.95	0.00	0.96
cmp.similarity	0.02	0.00	0.01
conMA	0.05	0.01	0.06
connections	0.25	0.01	0.26
datablock	0.38	0.00	0.37
datablock2ma	0.03	0.00	0.03
db.explain	0.06	0.00	0.06
db.subset	0.02	0.00	0.02
dbTransaction	0.03	0.02	0.05
desc2fp	0.24	0.00	0.24
exactMassOB	0.93	0.02	1.59
findCompounds	4.36	0.07	4.43
findCompoundsByName	0.71	0.02	0.73
fingerprintOB	0.02	0.00	0.02
fold	0	0	0
foldCount	0	0	0
fp2bit	0.51	0.01	0.53
fpSim	0.68	0.05	0.71
fptype	0	0	0
fromNNMatrix	1.45	0.00	1.46
genAPDescriptors	0.01	0.00	0.01
generate3DCoords	24.79	0.02	25.30
getAllCompoundIds	0.50	0.01	0.52
getCompoundFeatures	0.59	0.00	0.59
getCompoundNames	0.54	0.00	0.54
getCompounds	0.63	0.02	0.64
getIds	0	0	0
grepSDFset	0.05	0.00	0.05
groups	0.16	0.00	0.15
header	0.14	0.00	0.14
initDb	0.03	0.00	0.03
jarvisPatrick	2.59	0.00	2.59
jobToken-class	0	0	0
launchCMTool	0	0	0
listCMTools	0	0	0
listFeatures	0.52	0.01	0.53
loadSdf	3.71	0.00	3.90
makeUnique	0.02	0.00	0.01
maximallyDissimilar	0.45	0.00	0.46
nearestNeighbors	1.82	0.00	1.82
numBits	0	0	0
obmol	0.05	0.00	0.05
parBatchByIndex	0	0	0
plotStruc	0.33	0.00	0.33
propOB	0	0	0
pubchemFPencoding	0.00	0.01	0.02
read.AP	0.01	0.00	0.01
read.SDFindex	0.02	0.00	0.02
read.SDFset	1.10	0.00	1.11
read.SDFstr	1.33	0.00	1.33
read.SMIset	0	0	0
regenerateCoords	0	0	0
result	0	0	0
rings	1.13	0.02	1.14
sdf.subset	0	0	0
sdf.visualize	0.03	0.00	0.03
sdf2ap	0.81	0.03	0.85
sdf2list	0.06	0.00	0.06
sdf2smiles	0	0	0
sdf2str	0.05	0.00	0.05
sdfStream	0.03	0.00	0.03
sdfid	0.03	0.00	0.04
sdfsample	0.1	0.0	0.1
sdfstr2list	1.61	0.13	1.95
searchSim	0	0	0
searchString	0	0	0
selectInBatches	0	0	0
setPriorities	0	0	0
smartsSearchOB	0	0	0
smiles2sdf	0	0	0
smisample	0.02	0.00	0.01
status	0	0	0
toolDetails	0	0	0
trimNeighbors	2.88	0.00	2.89
validSDF	0.02	0.01	0.03
view	0.08	0.00	0.08
write.SDF	0.29	0.00	0.30
write.SDFsplit	0.02	0.00	0.01
write.SMI	0	0	0

BioC 3.0: CHECK report for ChemmineR on moscato1

Summary

Command output