BioC 3.0: CHECK report for ChemmineR on zin1

Package: ChemmineR

Version: 2.18.1

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.18.1.tar.gz

StartedAt: 2015-04-09 22:23:06 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:25:34 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 148.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChemmineR.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.18.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/ChemmineR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [12s/12s] 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 ... [53s/54s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
generate3DCoords 15.281  0.004  15.335
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [33s/33s]
 [33s/34s] 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
  ‘/home/biocbuild/bbs-3.0-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c DisjointSets.cpp -o DisjointSets.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c formats.cc -o formats.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c molecule.cc -o molecule.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c script.cc -o script.o
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c similarity.cc -o similarity.o
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/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 -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/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	0.444	0.056	0.501
APset-class	0.364	0.024	0.389
FP-class	0.088	0.000	0.090
FPset-class	0.436	0.004	0.441
SDF-class	0.056	0.004	0.061
SDF2apcmp	0.024	0.000	0.022
SDFset-class	0.448	0.016	0.467
SDFset2SDF	0.124	0.004	0.127
SDFset2list	0.056	0.012	0.071
SDFstr-class	0.280	0.000	0.278
SMI-class	0.004	0.000	0.003
SMIset-class	0.008	0.000	0.007
addDescriptorType	0	0	0
addNewFeatures	2.856	0.020	2.880
ap	0.160	0.008	0.167
apfp	0.004	0.000	0.003
apset	0.004	0.000	0.005
apset2descdb	0.380	0.048	0.436
atomblock	0.100	0.012	0.114
atomcount	0.212	0.000	0.209
atomprop	0.004	0.000	0.004
atomsubset	0.028	0.000	0.029
batchByIndex	0.000	0.000	0.001
bondblock	0.104	0.004	0.105
bonds	0.032	0.000	0.032
browseJob	0.000	0.000	0.001
bufferLines	0.000	0.000	0.001
bufferResultSet	0.000	0.000	0.001
byCluster	0.896	0.000	0.900
canonicalNumbering	0.388	0.016	0.819
canonicalize	0.044	0.000	0.045
cid	0.020	0.000	0.024
cluster.sizestat	0.592	0.008	0.601
cluster.visualize	0.832	0.000	0.831
cmp.cluster	2.428	0.020	2.479
cmp.duplicated	0.064	0.000	0.064
cmp.parse	0.028	0.000	0.028
cmp.parse1	0.000	0.000	0.001
cmp.search	0.816	0.008	0.826
cmp.similarity	0.020	0.004	0.023
conMA	0.056	0.012	0.066
connections	0.208	0.016	0.249
datablock	0.292	0.000	0.292
datablock2ma	0.032	0.000	0.035
db.explain	0.048	0.012	0.060
db.subset	0.004	0.000	0.004
dbTransaction	0.032	0.008	0.041
desc2fp	0.124	0.000	0.124
exactMassOB	0.756	0.000	0.758
findCompounds	2.541	0.016	2.561
findCompoundsByName	0.356	0.000	0.356
fingerprintOB	0.000	0.000	0.001
fold	0.000	0.000	0.001
foldCount	0.000	0.004	0.002
fp2bit	0.392	0.016	0.407
fpSim	0.420	0.004	0.423
fptype	0.000	0.000	0.001
fromNNMatrix	0.920	0.000	0.921
genAPDescriptors	0.016	0.000	0.016
generate3DCoords	15.281	0.004	15.335
getAllCompoundIds	0.344	0.008	0.354
getCompoundFeatures	2.592	0.012	2.618
getCompoundNames	0.480	0.000	0.479
getCompounds	0.360	0.012	0.370
getIds	0.000	0.000	0.001
grepSDFset	0.048	0.000	0.047
groups	0.216	0.000	0.213
header	0.100	0.004	0.104
initDb	0.036	0.004	0.040
jarvisPatrick	2.184	0.004	2.241
jobToken-class	0.000	0.004	0.001
launchCMTool	0.000	0.000	0.001
listCMTools	0.000	0.000	0.001
listFeatures	0.432	0.004	0.483
loadSdf	2.924	0.008	2.943
makeUnique	0.016	0.000	0.017
maximallyDissimilar	0.324	0.004	0.327
nearestNeighbors	1.196	0.000	1.196
numBits	0.004	0.000	0.001
obmol	0.040	0.000	0.039
parBatchByIndex	0.000	0.000	0.001
plotStruc	0.280	0.000	0.281
propOB	0.000	0.000	0.001
pubchemFPencoding	0.000	0.004	0.003
read.AP	0.020	0.000	0.017
read.SDFindex	0.016	0.000	0.017
read.SDFset	0.672	0.004	0.701
read.SDFstr	0.857	0.000	0.857
read.SMIset	0.000	0.004	0.002
regenerateCoords	0.000	0.000	0.001
result	0.004	0.000	0.001
rings	0.620	0.000	0.622
sdf.subset	0	0	0
sdf.visualize	0.016	0.000	0.016
sdf2ap	0.348	0.040	0.388
sdf2list	0.032	0.000	0.029
sdf2smiles	0.000	0.000	0.001
sdf2str	0.032	0.000	0.030
sdfStream	0.016	0.000	0.017
sdfid	0.020	0.000	0.018
sdfsample	0.060	0.000	0.058
sdfstr2list	0.844	0.144	0.992
searchSim	0.000	0.000	0.001
searchString	0	0	0
selectInBatches	0.000	0.000	0.002
setPriorities	0	0	0
smartsSearchOB	0.004	0.000	0.000
smiles2sdf	0.000	0.000	0.001
smisample	0.004	0.000	0.004
status	0.000	0.000	0.001
toolDetails	0.000	0.000	0.001
trimNeighbors	1.776	0.004	1.797
validSDF	0.020	0.000	0.023
view	0.064	0.000	0.065
write.SDF	0.200	0.000	0.201
write.SDFsplit	0.016	0.000	0.017
write.SMI	0.004	0.000	0.002