BioC 3.4: CHECK report for ChemmineR on morelia

Package: ChemmineR

Version: 2.26.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChemmineR_2.26.1.tar.gz

StartedAt: 2017-04-14 23:43:08 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:45:39 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 151.2 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 ChemmineR_2.26.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ChemmineR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.26.1’
* 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-3.4-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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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-3.4-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	0.466	0.077	0.544
APset-class	0.318	0.067	0.385
ExtSDF-class	0.001	0.000	0.001
FP-class	0.071	0.002	0.073
FPset-class	0.302	0.022	0.324
SDF-class	0.081	0.006	0.089
SDF2apcmp	0.027	0.002	0.029
SDFset-class	0.450	0.028	0.479
SDFset2SDF	0.118	0.007	0.125
SDFset2list	0.057	0.025	0.082
SDFstr-class	0.310	0.004	0.315
SMI-class	0.003	0.000	0.003
SMIset-class	0.006	0.001	0.007
addDescriptorType	0.000	0.001	0.001
addNewFeatures	3.009	0.137	3.431
ap	0.176	0.012	0.188
apfp	0.002	0.001	0.003
apset	0.003	0.001	0.004
apset2descdb	0.342	0.064	0.406
atomblock	0.111	0.017	0.129
atomcount	0.201	0.007	0.208
atomprop	0.003	0.000	0.004
atomsubset	0.032	0.001	0.034
batchByIndex	0.001	0.000	0.001
bondblock	0.126	0.010	0.136
bonds	0.040	0.002	0.043
browseJob	0.001	0.001	0.001
bufferLines	0.001	0.000	0.000
bufferResultSet	0.002	0.000	0.002
byCluster	0.991	0.007	0.999
canonicalNumbering	0.787	0.064	2.627
canonicalize	0.047	0.002	0.050
cid	0.031	0.001	0.032
cluster.sizestat	0.648	0.006	0.654
cluster.visualize	0.708	0.008	0.715
cmp.cluster	2.189	0.024	2.216
cmp.duplicated	0.048	0.001	0.050
cmp.parse	0.029	0.001	0.031
cmp.parse1	0.001	0.000	0.001
cmp.search	0.884	0.017	0.901
cmp.similarity	0.025	0.001	0.026
conMA	0.071	0.009	0.080
connections	0.214	0.004	0.312
datablock	0.329	0.009	0.338
datablock2ma	0.043	0.002	0.046
db.explain	0.071	0.004	0.076
db.subset	0.004	0.000	0.005
dbTransaction	0.030	0.010	0.042
desc2fp	0.113	0.002	0.116
draw_sdf	0.557	0.033	0.588
exactMassOB	0.903	0.004	0.908
findCompounds	2.566	0.029	2.600
findCompoundsByName	0.354	0.010	0.366
fingerprintOB	0.000	0.000	0.001
fold	0.001	0.001	0.001
foldCount	0.001	0.000	0.001
fp2bit	0.496	0.013	0.510
fpSim	0.313	0.005	0.319
fptype	0.001	0.000	0.002
fromNNMatrix	0.768	0.007	0.776
genAPDescriptors	0.019	0.000	0.021
genParameters	0.677	0.008	0.686
generate3DCoords	0.000	0.000	0.001
getAllCompoundIds	0.351	0.011	0.364
getCompoundFeatures	2.142	0.024	2.169
getCompoundNames	0.350	0.010	0.361
getCompounds	0.365	0.014	0.391
getIds	0.001	0.001	0.000
grepSDFset	0.063	0.001	0.064
groups	0.134	0.004	0.138
header	0.099	0.003	0.102
initDb	0.111	0.006	0.119
jarvisPatrick	1.746	0.064	1.812
jobToken-class	0.001	0.000	0.001
launchCMTool	0.001	0.001	0.000
listCMTools	0	0	0
listFeatures	0.411	0.009	0.428
loadSdf	2.510	0.038	2.551
makeUnique	0.014	0.001	0.015
maximallyDissimilar	0.209	0.001	0.210
nearestNeighbors	0.811	0.012	0.822
numBits	0.002	0.000	0.001
obmol	0.041	0.001	0.042
parBatchByIndex	0.001	0.001	0.002
plotStruc	0.290	0.006	4.241
propOB	0.000	0.000	0.001
pubchemFPencoding	0.003	0.001	0.005
read.AP	0.013	0.001	0.013
read.SDFindex	0.020	0.001	0.022
read.SDFset	0.726	0.002	0.729
read.SDFstr	0.721	0.002	0.724
read.SMIset	0.002	0.000	0.003
regenerateCoords	0.001	0.000	0.001
result	0.000	0.000	0.001
rings	0.489	0.007	1.257
sdf.subset	0	0	0
sdf.visualize	0.029	0.002	0.030
sdf2ap	0.341	0.056	1.024
sdf2list	0.027	0.009	0.037
sdf2smiles	0.001	0.000	0.000
sdf2str	0.046	0.004	0.051
sdfStream	0.017	0.001	0.017
sdfid	0.024	0.001	0.025
sdfsample	0.061	0.003	0.064
sdfstr2list	1.321	0.286	1.626
searchSim	0.000	0.000	0.001
searchString	0	0	0
selectInBatches	0.002	0.000	0.002
setPriorities	0.001	0.000	0.000
smartsSearchOB	0.001	0.000	0.001
smiles2sdf	0.001	0.000	0.001
smisample	0.004	0.000	0.005
status	0.001	0.000	0.001
toolDetails	0.001	0.000	0.001
trimNeighbors	1.457	0.066	1.524
validSDF	0.016	0.001	0.016
view	0.043	0.002	0.045
write.SDF	0.144	0.004	0.147
write.SDFsplit	0.015	0.001	0.015
write.SMI	0.002	0.001	0.002