BioC 3.5: 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_2.27.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ChemmineR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘2.27.1’
* 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 ... 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 global function definition for
  ‘write.table’
.data.frame.to.str: no visible binding for global variable ‘string’
.parseV3000: no visible binding for global variable ‘AW’
.rings: no visible global function definition for ‘combn’
applyOptions: no visible global function definition for ‘convertFormat’
browseJob: no visible global function definition for ‘browseURL’
canonicalNumbering: no visible global function definition for
  ‘canonicalNumbering_OB’
canonicalNumberingOB: no visible global function definition for
  ‘canonicalNumbering_OB’
cluster.visualize: no visible global function definition for ‘rainbow’
cluster.visualize: no visible global function definition for ‘pdf’
cluster.visualize: no visible global function definition for
  ‘postscript’
cluster.visualize: no visible global function definition for ‘dev.off’
concatenate_plots: no visible binding for global variable ‘arrangeGrob’
desc2fp: no visible global function definition for ‘data’
draw_sdf: no visible global function definition for ‘rgb’
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’
getCompoundFeatures : <anonymous>: no visible global function
  definition for ‘write.table’
getCompounds: no visible global function definition for ‘str’
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’
listCMTools: no visible global function definition for ‘read.table’
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’
read.AP: no visible global function definition for ‘read.delim’
sdf2OBMol: no visible global function definition for ‘forEachMol’
sdf2smiles: no visible global function definition for ‘convertFormat’
sdf2smilesOB: no visible global function definition for ‘convertFormat’
sdfStream: no visible global function definition for ‘write.table’
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’
write.SMI: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  AW C1 C1.1 C2 C2.1 arrangeGrob browseURL canonicalNumbering_OB
  clusterApplyLB clusterExport combn convertFormat convertFormatFile
  data dev.off error exactMass_OB fingerprint_OB fmcs forEachMol pdf
  postgresqlCopyInDataframe postgresqlQuoteId postgresqlTableRef
  postgresqlgetResult postgresqlpqExec postscript prop_OB rainbow
  rasterGrob read.delim read.table readPNG rgb smartsSearch_OB str
  string write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "postscript", "rainbow",
             "rgb")
  importFrom("utils", "browseURL", "combn", "data", "read.delim",
             "read.table", "str", "write.table")
to your NAMESPACE file.
* 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’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.5-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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-3.5-bioc/meat/ChemmineR.Rcheck/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChemmineR)

name	user	system	elapsed
AP-class	0.496	0.056	0.589
APset-class	0.634	0.045	0.702
ExtSDF-class	0.001	0.001	0.001
FP-class	0.085	0.004	0.089
FPset-class	0.424	0.025	0.449
SDF-class	0.065	0.007	0.093
SDF2apcmp	0.021	0.000	0.022
SDFset-class	0.432	0.022	0.455
SDFset2SDF	0.134	0.008	0.141
SDFset2list	0.071	0.033	0.105
SDFstr-class	0.323	0.007	0.330
SMI-class	0.003	0.001	0.005
SMIset-class	0.007	0.001	0.008
addDescriptorType	0.001	0.000	0.001
addNewFeatures	3.683	0.102	4.154
ap	0.082	0.008	0.098
apfp	0.002	0.001	0.002
apset	0.005	0.001	0.006
apset2descdb	0.300	0.061	0.376
atomblock	0.135	0.016	0.150
atomcount	0.196	0.004	0.209
atomprop	0.004	0.001	0.005
atomsubset	0.176	0.002	0.177
batchByIndex	0.001	0.000	0.001
bondblock	0.082	0.008	0.090
bonds	0.040	0.003	0.042
browseJob	0.001	0.000	0.001
bufferLines	0.001	0.000	0.001
bufferResultSet	0.002	0.000	0.002
byCluster	0.677	0.007	0.684
canonicalNumbering	0.628	0.063	1.911
canonicalize	0.114	0.001	0.115
cid	0.027	0.001	0.028
cluster.sizestat	0.474	0.006	0.480
cluster.visualize	0.617	0.026	0.644
cmp.cluster	2.112	0.054	2.218
cmp.duplicated	0.040	0.001	0.042
cmp.parse	0.031	0.002	0.033
cmp.parse1	0.001	0.000	0.000
cmp.search	0.576	0.008	0.583
cmp.similarity	0.018	0.001	0.019
conMA	0.061	0.011	0.072
connections	0.278	0.005	0.335
datablock	0.261	0.008	0.268
datablock2ma	0.093	0.002	0.095
db.explain	0.075	0.006	0.082
db.subset	0.004	0.001	0.006
dbTransaction	0.027	0.004	0.032
desc2fp	0.150	0.003	0.153
draw_sdf	1.775	0.037	1.858
exactMassOB	0.729	0.003	0.748
findCompounds	2.592	0.031	4.408
findCompoundsByName	0.359	0.009	0.408
fingerprintOB	0	0	0
fold	0.001	0.000	0.001
foldCount	0.022	0.000	0.023
fp2bit	0.254	0.013	0.267
fpSim	0.381	0.009	0.391
fptype	0.001	0.000	0.000
fromNNMatrix	0.715	0.034	0.750
genAPDescriptors	0.013	0.001	0.013
genParameters	0.452	0.003	0.458
generate3DCoords	0	0	0
getAllCompoundIds	0.384	0.008	0.394
getCompoundFeatures	2.123	0.023	2.801
getCompoundNames	0.252	0.009	0.446
getCompounds	0.331	0.011	1.474
getIds	0	0	0
grepSDFset	0.098	0.001	0.119
groups	0.202	0.004	1.106
header	0.063	0.002	0.126
initDb	0.020	0.004	0.237
jarvisPatrick	1.378	0.027	2.622
jobToken-class	0.001	0.000	0.001
launchCMTool	0.001	0.000	0.001
listCMTools	0.000	0.001	0.010
listFeatures	0.265	0.009	1.157
loadSdf	2.473	0.035	3.709
makeUnique	0.014	0.001	0.026
maximallyDissimilar	0.162	0.002	0.811
nearestNeighbors	0.729	0.004	0.828
numBits	0.000	0.000	0.001
obmol	0.034	0.001	0.117
parBatchByIndex	0.000	0.000	0.001
plotStruc	0.260	0.005	0.386
propOB	0	0	0
pubchemFPencoding	0.003	0.000	0.012
read.AP	0.022	0.001	0.029
read.SDFindex	0.014	0.001	0.647
read.SDFset	0.548	0.001	0.580
read.SDFstr	0.827	0.004	0.951
read.SMIset	0.001	0.000	0.005
regenerateCoords	0.001	0.000	0.040
result	0.001	0.000	0.000
rings	0.537	0.008	1.219
sdf.subset	0.001	0.000	0.000
sdf.visualize	0.015	0.001	0.043
sdf2ap	0.278	0.056	0.505
sdf2list	0.026	0.009	0.034
sdf2smiles	0.001	0.000	0.001
sdf2str	0.042	0.004	0.058
sdfStream	0.026	0.001	0.027
sdfid	0.014	0.001	0.015
sdfsample	0.039	0.002	0.041
sdfstr2list	0.941	0.203	2.918
searchSim	0.001	0.001	0.000
searchString	0	0	0
selectInBatches	0.001	0.000	0.001
setPriorities	0	0	0
smartsSearchOB	0.001	0.001	0.001
smiles2sdf	0	0	0
smisample	0.002	0.000	0.003
status	0.001	0.000	0.001
toolDetails	0	0	0
trimNeighbors	0.929	0.002	0.931
validSDF	0.016	0.001	0.015
view	0.059	0.003	0.062
write.SDF	0.134	0.003	0.137
write.SDFsplit	0.012	0.000	0.012
write.SMI	0.001	0.001	0.001

BioC 3.5: CHECK report for ChemmineR on oaxaca

Summary

Command output