BioC 3.5: CHECK report for ChemmineR on toluca2

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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 r72187)
* 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	0.738	0.079	0.824
APset-class	0.891	0.080	0.979
ExtSDF-class	0.002	0.001	0.002
FP-class	0.079	0.002	0.086
FPset-class	0.418	0.020	0.444
SDF-class	0.070	0.006	0.079
SDF2apcmp	0.025	0.001	0.026
SDFset-class	0.462	0.028	0.496
SDFset2SDF	0.130	0.008	0.140
SDFset2list	0.062	0.024	0.087
SDFstr-class	0.362	0.004	0.368
SMI-class	0.004	0.000	0.005
SMIset-class	0.007	0.001	0.008
addDescriptorType	0.001	0.000	0.001
addNewFeatures	4.423	0.096	4.607
ap	0.091	0.009	0.099
apfp	0.003	0.001	0.003
apset	0.005	0.001	0.006
apset2descdb	0.324	0.061	0.391
atomblock	0.125	0.014	0.139
atomcount	0.211	0.003	0.217
atomprop	0.004	0.000	0.005
atomsubset	0.151	0.002	0.154
batchByIndex	0.001	0.000	0.001
bondblock	0.098	0.007	0.106
bonds	0.036	0.003	0.038
browseJob	0.001	0.000	0.000
bufferLines	0.001	0.000	0.000
bufferResultSet	0.001	0.000	0.002
byCluster	0.740	0.012	0.752
canonicalNumbering	0.338	0.016	0.360
canonicalize	0.100	0.002	0.102
cid	0.026	0.001	0.027
cluster.sizestat	0.528	0.007	0.537
cluster.visualize	0.601	0.008	0.610
cmp.cluster	2.199	0.042	2.244
cmp.duplicated	0.054	0.001	0.056
cmp.parse	0.027	0.002	0.028
cmp.parse1	0	0	0
cmp.search	0.678	0.015	0.695
cmp.similarity	0.018	0.001	0.019
conMA	0.070	0.009	0.082
connections	0.265	0.003	0.277
datablock	0.280	0.007	0.288
datablock2ma	0.072	0.002	0.075
db.explain	0.064	0.005	0.069
db.subset	0.004	0.001	0.005
dbTransaction	0.025	0.003	0.028
desc2fp	0.142	0.003	0.149
draw_sdf	2.163	0.033	2.396
exactMassOB	0.744	0.003	0.822
findCompounds	3.459	0.024	3.705
findCompoundsByName	0.374	0.009	0.402
fingerprintOB	0.000	0.000	0.001
fold	0.002	0.000	0.002
foldCount	0.025	0.000	0.025
fp2bit	0.337	0.014	0.353
fpSim	0.503	0.010	0.518
fptype	0.001	0.000	0.002
fromNNMatrix	0.822	0.043	0.866
genAPDescriptors	0.021	0.001	0.022
genParameters	0.669	0.009	0.682
generate3DCoords	0.000	0.000	0.001
getAllCompoundIds	0.379	0.010	0.393
getCompoundFeatures	3.070	0.027	3.121
getCompoundNames	0.377	0.009	0.391
getCompounds	0.456	0.012	0.473
getIds	0.001	0.000	0.000
grepSDFset	0.118	0.001	0.119
groups	0.287	0.004	0.292
header	0.091	0.002	0.094
initDb	0.022	0.003	0.025
jarvisPatrick	2.095	0.025	2.139
jobToken-class	0.001	0.000	0.002
launchCMTool	0.001	0.001	0.001
listCMTools	0.001	0.000	0.001
listFeatures	0.410	0.010	0.428
loadSdf	3.420	0.036	3.506
makeUnique	0.021	0.001	0.023
maximallyDissimilar	0.260	0.001	0.262
nearestNeighbors	1.057	0.024	1.092
numBits	0.002	0.000	0.002
obmol	0.046	0.002	0.048
parBatchByIndex	0.001	0.000	0.001
plotStruc	0.326	0.006	0.336
propOB	0.001	0.000	0.001
pubchemFPencoding	0.004	0.000	0.004
read.AP	0.022	0.001	0.022
read.SDFindex	0.021	0.001	0.022
read.SDFset	0.835	0.003	0.844
read.SDFstr	1.189	0.007	1.200
read.SMIset	0.002	0.000	0.003
regenerateCoords	0.000	0.000	0.001
result	0.001	0.000	0.001
rings	0.734	0.008	0.745
sdf.subset	0.001	0.000	0.001
sdf.visualize	0.020	0.001	0.021
sdf2ap	0.469	0.061	0.536
sdf2list	0.029	0.008	0.037
sdf2smiles	0.000	0.000	0.001
sdf2str	0.037	0.004	0.042
sdfStream	0.020	0.001	0.022
sdfid	0.023	0.001	0.023
sdfsample	0.059	0.003	0.063
sdfstr2list	1.282	0.310	1.608
searchSim	0.001	0.000	0.001
searchString	0.000	0.000	0.001
selectInBatches	0.001	0.000	0.002
setPriorities	0.001	0.000	0.001
smartsSearchOB	0.001	0.000	0.001
smiles2sdf	0.001	0.000	0.001
smisample	0.003	0.001	0.004
status	0.001	0.000	0.001
toolDetails	0.000	0.000	0.001
trimNeighbors	1.318	0.013	1.358
validSDF	0.025	0.001	0.025
view	0.064	0.003	0.067
write.SDF	0.199	0.003	0.203
write.SDFsplit	0.021	0.000	0.021
write.SMI	0.002	0.000	0.003

BioC 3.5: CHECK report for ChemmineR on toluca2

Summary

Command output