BioC 3.2: CHECK report for ChemmineR on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChemmineR_2.21.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘2.21.7’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChemmineR’ can be installed ... [21s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘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
* 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’ ‘fmcsR’ ‘grid’ ‘png’ ‘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’
.parseV3000: no visible binding for global variable ‘AW’
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’
concatenate_plots: no visible binding for global variable ‘arrangeGrob’
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’
getDbConn: no visible global function definition for ‘error’
handle_raster: no visible global function definition for ‘readPNG’
handle_raster: no visible global function definition for ‘rasterGrob’
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’
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’
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’
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
File ‘ChemmineR/libs/ChemmineR.so’:
  Found ‘__ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Objects: ‘desc.o’, ‘formats.o’, ‘script.o’
  Found ‘__ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘cluster.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... [51s/52s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [24s/25s]
 [24s/26s] OK
* 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c DisjointSets.cpp -o DisjointSets.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&)’:
cluster.cc:118: warning: comparison between signed and unsigned integer expressions
cluster.cc:118: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘int contains(int, std::vector<int, std::allocator<int> >&)’:
cluster.cc:131: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXPREC*)’:
cluster.cc:284: warning: comparison between signed and unsigned integer expressions
cluster.cc:298: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘void loadNNList(int, int, SEXPREC*)’:
cluster.cc:314: warning: comparison between signed and unsigned integer expressions
cluster.cc:332: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘SEXPREC* jarvis_patrick(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
cluster.cc:390: warning: comparison between signed and unsigned integer expressions
cluster.cc: At global scope:
cluster.cc:49: warning: ‘void prepare_neighbors(const char*, int, int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c cstrsplit.cc -o cstrsplit.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXPREC*)’:
desc.cc:249: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function ‘SEXPREC* uniquifyAtomPairs(SEXPREC*)’:
fingerprints.cc:138: warning: comparison between signed and unsigned integer expressions
fingerprints.cc:145: warning: comparison between signed and unsigned integer expressions
fingerprints.cc:158: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c formats.cc -o formats.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c molecule.cc -o molecule.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c r_wrap.cc -o r_wrap.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c script.cc -o script.o
desc.h:39: warning: ‘elements’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c similarity.cc -o similarity.o
desc.h:39: warning: ‘elements’ defined but not used
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck/ChemmineR/libs
** 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
* DONE (ChemmineR)

name	user	system	elapsed
AP-class	0.448	0.101	0.550
APset-class	0.435	0.086	0.521
ExtSDF-class	0.002	0.000	0.002
FP-class	0.193	0.003	0.196
FPset-class	0.341	0.034	0.376
SDF-class	0.091	0.009	0.101
SDF2apcmp	0.027	0.001	0.027
SDFset-class	0.541	0.040	0.582
SDFset2SDF	0.155	0.010	0.166
SDFset2list	0.078	0.043	0.120
SDFstr-class	0.520	0.004	0.523
SMI-class	0.003	0.001	0.004
SMIset-class	0.008	0.001	0.009
addDescriptorType	0.001	0.001	0.000
addNewFeatures	3.669	0.179	3.871
ap	0.132	0.017	0.150
apfp	0.003	0.001	0.004
apset	0.006	0.001	0.007
apset2descdb	0.433	0.094	0.527
atomblock	0.133	0.021	0.154
atomcount	0.270	0.007	0.276
atomprop	0.004	0.001	0.006
atomsubset	0.033	0.001	0.035
batchByIndex	0.001	0.000	0.001
bondblock	0.126	0.013	0.139
bonds	0.037	0.003	0.040
browseJob	0.001	0.001	0.002
bufferLines	0	0	0
bufferResultSet	0.002	0.000	0.002
byCluster	1.139	0.005	1.145
canonicalNumbering	0.960	0.056	1.370
canonicalize	0.064	0.001	0.065
cid	0.026	0.001	0.027
cluster.sizestat	0.869	0.011	0.880
cluster.visualize	1.098	0.014	1.112
cmp.cluster	2.790	0.043	2.832
cmp.duplicated	0.048	0.001	0.049
cmp.parse	0.032	0.002	0.034
cmp.parse1	0.001	0.000	0.001
cmp.search	0.894	0.016	0.910
cmp.similarity	0.024	0.001	0.026
conMA	0.072	0.013	0.085
connections	0.321	0.006	0.406
datablock	0.351	0.009	0.360
datablock2ma	0.054	0.002	0.055
db.explain	0.088	0.007	0.095
db.subset	0.005	0.001	0.006
dbTransaction	0.086	0.008	0.094
desc2fp	0.146	0.005	0.151
draw_sdf	0.584	0.075	0.664
exactMassOB	1.083	0.026	1.110
findCompounds	2.924	0.072	3.003
findCompoundsByName	0.497	0.023	0.648
fingerprintOB	0.001	0.000	0.001
fold	0.002	0.000	0.002
foldCount	0.002	0.000	0.001
fp2bit	0.658	0.030	0.689
fpSim	0.542	0.015	0.557
fptype	0.002	0.000	0.001
fromNNMatrix	1.133	0.011	1.145
genAPDescriptors	0.020	0.001	0.022
genParameters	0.764	0.004	0.768
generate3DCoords	0.001	0.000	0.001
getAllCompoundIds	0.660	0.019	0.680
getCompoundFeatures	2.912	0.066	2.984
getCompoundNames	0.512	0.019	0.535
getCompounds	0.508	0.015	0.526
getIds	0.001	0.000	0.001
grepSDFset	0.057	0.001	0.059
groups	0.172	0.008	0.181
header	0.146	0.006	0.153
initDb	0.087	0.005	0.093
jarvisPatrick	2.783	0.172	2.960
jobToken-class	0.001	0.000	0.001
launchCMTool	0.000	0.000	0.001
listCMTools	0.000	0.000	0.001
listFeatures	0.530	0.020	0.555
loadSdf	3.475	0.068	3.543
makeUnique	0.021	0.001	0.022
maximallyDissimilar	0.345	0.006	0.351
nearestNeighbors	1.412	0.095	1.509
numBits	0.002	0.000	0.001
obmol	0.076	0.003	0.079
parBatchByIndex	0.001	0.000	0.002
plotStruc	0.339	0.013	0.351
propOB	0.001	0.000	0.001
pubchemFPencoding	0.004	0.001	0.005
read.AP	0.020	0.001	0.021
read.SDFindex	0.019	0.001	0.021
read.SDFset	0.899	0.006	0.907
read.SDFstr	1.194	0.006	1.201
read.SMIset	0.002	0.001	0.003
regenerateCoords	0.001	0.000	0.001
result	0.001	0.000	0.001
rings	0.657	0.014	0.671
sdf.subset	0.000	0.000	0.001
sdf.visualize	0.020	0.001	0.021
sdf2ap	0.539	0.107	0.648
sdf2list	0.033	0.012	0.045
sdf2smiles	0.001	0.001	0.000
sdf2str	0.042	0.004	0.046
sdfStream	0.021	0.002	0.023
sdfid	0.021	0.001	0.023
sdfsample	0.067	0.003	0.070
sdfstr2list	1.951	0.427	2.392
searchSim	0.000	0.000	0.001
searchString	0.001	0.001	0.000
selectInBatches	0.003	0.000	0.003
setPriorities	0.001	0.000	0.001
smartsSearchOB	0.001	0.000	0.000
smiles2sdf	0.001	0.000	0.001
smisample	0.007	0.001	0.008
status	0.000	0.000	0.001
toolDetails	0.001	0.000	0.001
trimNeighbors	2.145	0.125	2.270
validSDF	0.023	0.001	0.025
view	0.064	0.004	0.069
write.SDF	0.229	0.006	0.236
write.SDFsplit	0.019	0.000	0.019
write.SMI	0.002	0.000	0.003

BioC 3.2: CHECK report for ChemmineR on perceval

Summary

Command output