BioC 3.2: CHECK report for ChemmineR on oaxaca

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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_2.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.22.0’
* 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 ... [17s/22s] 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’ ‘RPostgreSQL’ ‘RSQLite’ ‘fmcsR’ ‘grid’
  ‘png’ ‘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 ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
  -stdlib=libstdc++
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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 ... [44s/45s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [20s/23s]
 [20s/23s] 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, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c DisjointSets.cpp -o DisjointSets.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c cluster.cc -o cluster.o
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
            ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c cstrsplit.cc -o cstrsplit.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c desc.cc -o desc.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c fingerprints.cc -o fingerprints.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c formats.cc -o formats.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c molecule.cc -o molecule.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c r_wrap.cc -o r_wrap.o
r_wrap.cc:1689:14: warning: explicitly assigning a variable of type 'void *' to itself [-Wself-assign]
  clientdata = clientdata;
  ˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c script.cc -o script.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c similarity.cc -o similarity.o
clang++ -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 -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -stdlib=libstdc++ -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	0.404	0.087	0.505
APset-class	0.400	0.068	0.475
ExtSDF-class	0.002	0.000	0.002
FP-class	0.142	0.001	0.145
FPset-class	0.342	0.021	0.367
SDF-class	0.083	0.006	0.094
SDF2apcmp	0.024	0.001	0.025
SDFset-class	0.543	0.032	0.601
SDFset2SDF	0.161	0.008	0.176
SDFset2list	0.066	0.028	0.095
SDFstr-class	0.373	0.006	0.387
SMI-class	0.004	0.000	0.006
SMIset-class	0.008	0.000	0.009
addDescriptorType	0	0	0
addNewFeatures	3.411	0.130	4.201
ap	0.111	0.012	0.122
apfp	0.003	0.001	0.004
apset	0.010	0.002	0.012
apset2descdb	0.344	0.068	0.412
atomblock	0.135	0.015	0.149
atomcount	0.236	0.004	0.240
atomprop	0.004	0.001	0.005
atomsubset	0.035	0.001	0.036
batchByIndex	0.001	0.000	0.001
bondblock	0.139	0.010	0.149
bonds	0.041	0.002	0.044
browseJob	0.001	0.001	0.002
bufferLines	0.001	0.000	0.001
bufferResultSet	0.002	0.000	0.002
byCluster	0.882	0.016	0.899
canonicalNumbering	0.783	0.024	1.062
canonicalize	0.052	0.000	0.073
cid	0.022	0.000	0.023
cluster.sizestat	0.613	0.007	0.620
cluster.visualize	0.783	0.008	0.792
cmp.cluster	2.402	0.041	2.469
cmp.duplicated	0.054	0.001	0.055
cmp.parse	0.028	0.000	0.037
cmp.parse1	0.000	0.000	0.001
cmp.search	0.704	0.027	0.733
cmp.similarity	0.021	0.001	0.023
conMA	0.073	0.010	0.106
connections	0.275	0.008	0.437
datablock	0.306	0.007	0.313
datablock2ma	0.051	0.001	0.052
db.explain	0.053	0.005	0.059
db.subset	0.004	0.001	0.004
dbTransaction	0.049	0.004	0.054
desc2fp	0.117	0.003	0.120
draw_sdf	0.426	0.034	0.462
exactMassOB	0.903	0.004	0.908
findCompounds	2.773	0.024	2.802
findCompoundsByName	0.431	0.010	0.443
fingerprintOB	0.000	0.000	0.001
fold	0.001	0.000	0.002
foldCount	0.002	0.000	0.002
fp2bit	0.496	0.014	0.510
fpSim	0.393	0.005	0.399
fptype	0.001	0.000	0.001
fromNNMatrix	0.933	0.008	0.941
genAPDescriptors	0.022	0.000	0.023
genParameters	0.774	0.003	0.778
generate3DCoords	0	0	0
getAllCompoundIds	0.564	0.010	0.578
getCompoundFeatures	2.630	0.030	2.699
getCompoundNames	0.438	0.010	0.450
getCompounds	0.460	0.010	0.473
getIds	0.001	0.000	0.001
grepSDFset	0.05	0.00	0.05
groups	0.159	0.004	0.163
header	0.138	0.003	0.141
initDb	0.051	0.005	0.058
jarvisPatrick	2.397	0.014	2.413
jobToken-class	0.002	0.000	0.002
launchCMTool	0.001	0.001	0.001
listCMTools	0.001	0.000	0.001
listFeatures	0.447	0.009	0.458
loadSdf	2.973	0.034	3.012
makeUnique	0.023	0.000	0.023
maximallyDissimilar	0.296	0.001	0.296
nearestNeighbors	1.286	0.008	1.295
numBits	0.001	0.000	0.002
obmol	0.047	0.001	0.048
parBatchByIndex	0.001	0.000	0.001
plotStruc	0.331	0.006	0.338
propOB	0.001	0.000	0.001
pubchemFPencoding	0.004	0.000	0.003
read.AP	0.020	0.001	0.020
read.SDFindex	0.023	0.001	0.023
read.SDFset	0.859	0.002	0.861
read.SDFstr	1.215	0.003	1.220
read.SMIset	0.002	0.000	0.002
regenerateCoords	0.001	0.000	0.000
result	0.001	0.000	0.001
rings	0.575	0.007	0.584
sdf.subset	0.000	0.000	0.001
sdf.visualize	0.017	0.001	0.017
sdf2ap	0.399	0.060	0.461
sdf2list	0.032	0.009	0.042
sdf2smiles	0	0	0
sdf2str	0.038	0.003	0.042
sdfStream	0.023	0.000	0.023
sdfid	0.027	0.000	0.028
sdfsample	0.060	0.002	0.063
sdfstr2list	1.317	0.313	1.631
searchSim	0.001	0.000	0.001
searchString	0.000	0.000	0.001
selectInBatches	0.002	0.000	0.002
setPriorities	0.000	0.000	0.001
smartsSearchOB	0	0	0
smiles2sdf	0.001	0.000	0.001
smisample	0.004	0.000	0.004
status	0.000	0.000	0.001
toolDetails	0.001	0.000	0.001
trimNeighbors	1.807	0.012	1.821
validSDF	0.032	0.001	0.033
view	0.079	0.004	0.083
write.SDF	0.364	0.005	0.368
write.SDFsplit	0.022	0.000	0.022
write.SMI	0.002	0.000	0.003

BioC 3.2: CHECK report for ChemmineR on oaxaca

Summary

Command output