BioC 3.6: CHECK report for ChemmineR on veracruz1

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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_2.29.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘2.29.3’
* 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’ ‘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’
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_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 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
  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 ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘ChemmineR/libs/ChemmineR.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Objects: ‘desc.o’, ‘formats.o’, ‘script.o’
  Found ‘__ZNSt3__14coutE’, 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-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  -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  -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  -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  -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  -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  -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  -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  -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  -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  -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-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	0.657	0.080	0.755
APset-class	0.693	0.062	0.788
ExtSDF-class	0.001	0.000	0.001
FP-class	0.062	0.002	0.065
FPset-class	0.351	0.018	0.374
SDF-class	0.063	0.007	0.072
SDF2apcmp	0.020	0.001	0.021
SDFset-class	0.382	0.024	0.419
SDFset2SDF	0.102	0.008	0.109
SDFset2list	0.061	0.029	0.100
SDFstr-class	0.294	0.004	0.306
SMI-class	0.003	0.001	0.004
SMIset-class	0.004	0.001	0.006
addDescriptorType	0.001	0.000	0.000
addNewFeatures	3.699	0.102	3.979
ap	0.086	0.009	0.101
apfp	0.003	0.001	0.004
apset	0.005	0.001	0.006
apset2descdb	0.301	0.063	0.380
atomblock	0.110	0.014	0.129
atomcount	0.200	0.004	0.214
atomprop	0.004	0.001	0.004
atomsubset	0.113	0.002	0.116
batchByIndex	0.001	0.000	0.001
bondblock	0.078	0.009	0.088
bonds	0.037	0.002	0.040
browseJob	0.002	0.000	0.002
bufferLines	0.001	0.000	0.001
bufferResultSet	0.001	0.000	0.001
byCluster	0.688	0.012	0.731
canonicalNumbering	0.410	0.039	0.529
canonicalize	0.082	0.002	0.086
cid	0.019	0.001	0.020
cluster.sizestat	0.460	0.007	0.476
cluster.visualize	0.710	0.011	0.741
cmp.cluster	1.810	0.035	1.878
cmp.duplicated	0.048	0.001	0.049
cmp.parse	0.029	0.002	0.030
cmp.parse1	0	0	0
cmp.search	0.592	0.013	0.614
cmp.similarity	0.020	0.003	0.024
conMA	0.064	0.010	0.074
connections	0.230	0.005	0.239
datablock	0.186	0.007	0.196
datablock2ma	0.053	0.001	0.054
db.explain	0.047	0.003	0.051
db.subset	0.004	0.001	0.004
dbTransaction	0.017	0.003	0.020
desc2fp	0.106	0.003	0.111
draw_sdf	1.744	0.028	1.829
exactMassOB	0.561	0.003	0.583
findCompounds	2.735	0.017	2.866
findCompoundsByName	0.326	0.007	0.345
fingerprintOB	0.000	0.000	0.001
fold	0.001	0.000	0.001
foldCount	0.018	0.000	0.019
fp2bit	0.295	0.011	0.330
fpSim	0.312	0.006	0.321
fptype	0.001	0.000	0.002
fromNNMatrix	0.817	0.015	0.862
genAPDescriptors	0.019	0.001	0.020
genParameters	0.521	0.006	0.533
generate3DCoords	0.000	0.000	0.001
getAllCompoundIds	0.265	0.005	0.286
getCompoundFeatures	2.327	0.013	2.391
getCompoundNames	0.312	0.006	0.336
getCompounds	0.347	0.006	0.367
getIds	0.001	0.000	0.001
grepSDFset	0.111	0.002	0.113
groups	0.264	0.004	0.270
header	0.081	0.002	0.088
initDb	0.023	0.004	0.030
jarvisPatrick	1.997	0.011	2.079
jobToken-class	0.001	0.000	0.002
launchCMTool	0.001	0.000	0.001
listCMTools	0.001	0.001	0.001
listFeatures	0.323	0.006	0.345
loadSdf	2.765	0.018	2.877
makeUnique	0.021	0.000	0.021
maximallyDissimilar	0.222	0.001	0.224
nearestNeighbors	0.834	0.002	0.871
numBits	0.002	0.000	0.001
obmol	0.024	0.001	0.025
parBatchByIndex	0.001	0.000	0.001
plotStruc	0.293	0.006	0.339
propOB	0.000	0.001	0.001
pubchemFPencoding	0.003	0.000	0.004
read.AP	0.020	0.001	0.020
read.SDFindex	0.020	0.001	0.020
read.SDFset	0.671	0.003	0.692
read.SDFstr	0.991	0.004	1.022
read.SMIset	0.002	0.001	0.002
regenerateCoords	0.001	0.000	0.001
result	0.001	0.000	0.001
rings	0.542	0.005	0.574
sdf.subset	0.001	0.000	0.001
sdf.visualize	0.015	0.000	0.016
sdf2ap	0.329	0.065	0.430
sdf2list	0.029	0.009	0.039
sdf2smiles	0.001	0.000	0.000
sdf2str	0.034	0.004	0.042
sdfStream	0.025	0.001	0.026
sdfid	0.020	0.001	0.021
sdfsample	0.055	0.003	0.058
sdfstr2list	1.239	0.268	1.619
searchSim	0	0	0
searchString	0	0	0
selectInBatches	0.002	0.000	0.003
setPriorities	0.001	0.001	0.001
smartsSearchOB	0.001	0.000	0.001
smiles2sdf	0.001	0.000	0.001
smisample	0.003	0.001	0.004
status	0.000	0.000	0.001
toolDetails	0.000	0.000	0.001
trimNeighbors	1.182	0.016	1.356
validSDF	0.021	0.001	0.021
view	0.055	0.004	0.059
write.SDF	0.170	0.003	0.173
write.SDFsplit	0.019	0.001	0.019
write.SMI	0.003	0.000	0.003

BioC 3.6: CHECK report for ChemmineR on veracruz1

Summary

Command output