BioC 3.5: CHECK report for ChemmineR on veracruz2

Package: ChemmineR

Version: 2.28.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChemmineR_2.28.1.tar.gz

StartedAt: 2017-08-16 00:46:08 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:48:27 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 139.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChemmineR.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChemmineR_2.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ChemmineR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.28.1’
* 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  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -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  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -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  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -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  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -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  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -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  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -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  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -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  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c r_wrap.cc -o r_wrap.o
r_wrap.cc:1689:14: warning: explicitly assigning value of 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  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -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  -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -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	0.592	0.078	0.687
APset-class	0.709	0.069	0.801
ExtSDF-class	0.002	0.000	0.002
FP-class	0.068	0.003	0.070
FPset-class	0.387	0.021	0.425
SDF-class	0.069	0.007	0.084
SDF2apcmp	0.019	0.001	0.022
SDFset-class	0.376	0.029	0.410
SDFset2SDF	0.099	0.007	0.108
SDFset2list	0.055	0.029	0.085
SDFstr-class	0.328	0.005	0.347
SMI-class	0.004	0.001	0.004
SMIset-class	0.007	0.001	0.008
addDescriptorType	0.000	0.000	0.001
addNewFeatures	3.860	0.105	4.082
ap	0.102	0.013	0.119
apfp	0.003	0.001	0.003
apset	0.005	0.001	0.006
apset2descdb	0.291	0.068	0.375
atomblock	0.110	0.017	0.130
atomcount	0.205	0.004	0.219
atomprop	0.004	0.001	0.005
atomsubset	0.137	0.002	0.144
batchByIndex	0.001	0.000	0.001
bondblock	0.084	0.009	0.095
bonds	0.033	0.003	0.035
browseJob	0.001	0.000	0.001
bufferLines	0.001	0.000	0.001
bufferResultSet	0.001	0.000	0.001
byCluster	0.645	0.016	0.690
canonicalNumbering	0.368	0.038	0.470
canonicalize	0.110	0.002	0.114
cid	0.024	0.001	0.026
cluster.sizestat	0.456	0.007	0.475
cluster.visualize	0.611	0.017	0.649
cmp.cluster	1.881	0.029	1.952
cmp.duplicated	0.035	0.001	0.036
cmp.parse	0.026	0.001	0.029
cmp.parse1	0.001	0.000	0.001
cmp.search	0.591	0.009	0.611
cmp.similarity	0.017	0.002	0.023
conMA	0.064	0.008	0.074
connections	0.235	0.003	0.243
datablock	0.246	0.007	0.260
datablock2ma	0.071	0.002	0.073
db.explain	0.062	0.005	0.067
db.subset	0.004	0.001	0.005
dbTransaction	0.019	0.002	0.023
desc2fp	0.094	0.003	0.097
draw_sdf	1.774	0.027	1.841
exactMassOB	0.585	0.002	0.599
findCompounds	2.599	0.018	2.715
findCompoundsByName	0.337	0.007	0.350
fingerprintOB	0.001	0.000	0.000
fold	0.002	0.000	0.002
foldCount	0.019	0.000	0.019
fp2bit	0.328	0.009	0.348
fpSim	0.387	0.008	0.410
fptype	0.001	0.000	0.001
fromNNMatrix	0.791	0.017	0.827
genAPDescriptors	0.017	0.000	0.018
genParameters	0.494	0.003	0.516
generate3DCoords	0.000	0.000	0.001
getAllCompoundIds	0.329	0.007	0.345
getCompoundFeatures	2.380	0.015	2.514
getCompoundNames	0.260	0.006	0.276
getCompounds	0.327	0.005	0.351
getIds	0.001	0.001	0.001
grepSDFset	0.088	0.001	0.093
groups	0.225	0.003	0.241
header	0.084	0.002	0.093
initDb	0.018	0.002	0.021
jarvisPatrick	1.637	0.016	1.669
jobToken-class	0.000	0.000	0.001
launchCMTool	0.001	0.000	0.001
listCMTools	0.001	0.000	0.001
listFeatures	0.282	0.005	0.291
loadSdf	2.551	0.021	2.610
makeUnique	0.016	0.001	0.017
maximallyDissimilar	0.225	0.002	0.230
nearestNeighbors	0.972	0.013	0.994
numBits	0.001	0.000	0.001
obmol	0.033	0.001	0.038
parBatchByIndex	0.001	0.000	0.001
plotStruc	0.254	0.006	0.267
propOB	0.000	0.000	0.001
pubchemFPencoding	0.002	0.001	0.002
read.AP	0.014	0.001	0.014
read.SDFindex	0.018	0.001	0.019
read.SDFset	0.682	0.003	0.704
read.SDFstr	0.893	0.003	0.923
read.SMIset	0.001	0.000	0.002
regenerateCoords	0	0	0
result	0.001	0.000	0.001
rings	0.584	0.005	0.599
sdf.subset	0	0	0
sdf.visualize	0.018	0.001	0.019
sdf2ap	0.301	0.055	0.366
sdf2list	0.023	0.009	0.033
sdf2smiles	0.000	0.001	0.001
sdf2str	0.034	0.003	0.038
sdfStream	0.021	0.000	0.021
sdfid	0.020	0.001	0.021
sdfsample	0.053	0.003	0.057
sdfstr2list	1.164	0.289	1.487
searchSim	0.001	0.000	0.001
searchString	0.001	0.000	0.001
selectInBatches	0.002	0.004	0.005
setPriorities	0.001	0.000	0.000
smartsSearchOB	0.001	0.000	0.000
smiles2sdf	0.000	0.000	0.001
smisample	0.004	0.001	0.005
status	0.001	0.000	0.001
toolDetails	0.001	0.000	0.001
trimNeighbors	1.401	0.008	1.425
validSDF	0.023	0.001	0.024
view	0.059	0.004	0.065
write.SDF	0.159	0.003	0.162
write.SDFsplit	0.019	0.001	0.020
write.SMI	0.002	0.001	0.003