BioC 3.0: CHECK report for ChemmineR on perceval

Package: ChemmineR

Version: 2.18.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.18.1.tar.gz

StartedAt: 2015-04-09 23:38:43 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:42:30 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 226.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChemmineR.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ChemmineR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.18.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ChemmineR’ can be installed ... [16s/25s] 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
* 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
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’ ... OK
* checking examples ... [68s/75s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
generate3DCoords 14.012  0.041  14.267
addNewFeatures    3.952  0.296   8.804
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [40s/49s]
 [40s/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
  ‘/Users/biocbuild/bbs-3.0-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/3.1/Resources/library/Rcpp/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/3.1/Resources/library/Rcpp/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/3.1/Resources/library/Rcpp/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/3.1/Resources/library/Rcpp/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:137: warning: comparison between signed and unsigned integer expressions
fingerprints.cc:144: warning: comparison between signed and unsigned integer expressions
fingerprints.cc:157: 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/3.1/Resources/library/Rcpp/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/3.1/Resources/library/Rcpp/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/3.1/Resources/library/Rcpp/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/3.1/Resources/library/Rcpp/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/3.1/Resources/library/Rcpp/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 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-3.0-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	0.669	0.105	0.774
APset-class	0.449	0.089	0.549
FP-class	0.084	0.003	0.087
FPset-class	0.433	0.032	0.465
SDF-class	0.072	0.008	0.093
SDF2apcmp	0.032	0.001	0.033
SDFset-class	0.591	0.038	0.641
SDFset2SDF	0.180	0.010	0.191
SDFset2list	0.093	0.042	0.135
SDFstr-class	0.502	0.011	0.514
SMI-class	0.005	0.000	0.005
SMIset-class	0.010	0.001	0.011
addDescriptorType	0.000	0.000	0.001
addNewFeatures	3.952	0.296	8.804
ap	0.278	0.018	0.297
apfp	0.004	0.001	0.004
apset	0.007	0.001	0.008
apset2descdb	0.447	0.094	0.559
atomblock	0.145	0.020	0.164
atomcount	0.286	0.008	0.304
atomprop	0.005	0.001	0.005
atomsubset	0.036	0.002	0.038
batchByIndex	0.001	0.000	0.001
bondblock	0.137	0.012	0.150
bonds	0.042	0.003	0.045
browseJob	0.001	0.000	0.001
bufferLines	0.001	0.000	0.001
bufferResultSet	0.002	0.001	0.002
byCluster	1.225	0.007	1.233
canonicalNumbering	1.102	0.097	2.067
canonicalize	0.072	0.003	0.074
cid	0.026	0.001	0.027
cluster.sizestat	0.786	0.011	0.800
cluster.visualize	1.096	0.013	1.217
cmp.cluster	3.292	0.037	3.330
cmp.duplicated	0.052	0.002	0.054
cmp.parse	0.034	0.002	0.043
cmp.parse1	0.000	0.001	0.001
cmp.search	1.022	0.019	1.043
cmp.similarity	0.027	0.001	0.028
conMA	0.077	0.013	0.095
connections	0.346	0.014	0.419
datablock	0.429	0.011	0.440
datablock2ma	0.052	0.003	0.054
db.explain	0.097	0.008	0.104
db.subset	0.005	0.001	0.006
dbTransaction	0.093	0.011	0.157
desc2fp	0.134	0.005	0.145
exactMassOB	1.069	0.016	1.087
findCompounds	3.482	0.065	3.617
findCompoundsByName	0.504	0.025	0.592
fingerprintOB	0.000	0.000	0.001
fold	0.003	0.001	0.002
foldCount	0.003	0.000	0.003
fp2bit	0.657	0.024	0.691
fpSim	0.808	0.012	0.830
fptype	0.002	0.000	0.002
fromNNMatrix	1.172	0.004	1.176
genAPDescriptors	0.020	0.001	0.022
generate3DCoords	14.012	0.041	14.267
getAllCompoundIds	0.491	0.021	0.582
getCompoundFeatures	3.380	0.037	3.495
getCompoundNames	0.514	0.020	0.603
getCompounds	0.518	0.020	0.606
getIds	0.000	0.000	0.001
grepSDFset	0.071	0.001	0.073
groups	0.356	0.006	0.364
header	0.133	0.004	0.137
initDb	0.096	0.013	0.165
jarvisPatrick	2.764	0.014	2.778
jobToken-class	0.002	0.000	0.002
launchCMTool	0.001	0.000	0.001
listCMTools	0.001	0.000	0.001
listFeatures	0.569	0.024	0.649
loadSdf	3.705	0.043	3.879
makeUnique	0.022	0.001	0.022
maximallyDissimilar	0.392	0.001	0.393
nearestNeighbors	1.961	0.006	1.966
numBits	0.002	0.000	0.002
obmol	0.063	0.002	0.065
parBatchByIndex	0.001	0.000	0.001
plotStruc	0.379	0.013	0.421
propOB	0.000	0.000	0.001
pubchemFPencoding	0.004	0.001	0.005
read.AP	0.020	0.002	0.022
read.SDFindex	0.020	0.001	0.022
read.SDFset	0.813	0.003	0.817
read.SDFstr	1.201	0.005	1.206
read.SMIset	0.002	0.001	0.003
regenerateCoords	0.000	0.000	0.001
result	0.001	0.000	0.001
rings	0.705	0.005	0.722
sdf.subset	0.001	0.000	0.001
sdf.visualize	0.019	0.001	0.020
sdf2ap	0.529	0.089	0.624
sdf2list	0.042	0.012	0.053
sdf2smiles	0	0	0
sdf2str	0.044	0.005	0.049
sdfStream	0.022	0.001	0.023
sdfid	0.035	0.001	0.036
sdfsample	0.068	0.004	0.073
sdfstr2list	1.955	0.403	2.435
searchSim	0.000	0.000	0.001
searchString	0.001	0.000	0.001
selectInBatches	0.002	0.000	0.002
setPriorities	0.000	0.000	0.001
smartsSearchOB	0.001	0.001	0.000
smiles2sdf	0.001	0.000	0.001
smisample	0.006	0.000	0.007
status	0.001	0.000	0.001
toolDetails	0.001	0.000	0.001
trimNeighbors	2.199	0.007	2.206
validSDF	0.026	0.001	0.028
view	0.096	0.007	0.102
write.SDF	0.243	0.005	0.248
write.SDFsplit	0.019	0.001	0.020
write.SMI	0.002	0.001	0.003