BioC 3.3: CHECK report for ChemmineR on morelia

Package: ChemmineR

Version: 2.23.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChemmineR_2.23.5.tar.gz

StartedAt: 2016-04-21 00:07:49 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 00:11:05 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 196.4 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_2.23.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ChemmineR.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘2.23.5’
* 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 ... [18s/25s] 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’
insertDef: no visible global function definition for
  ‘dbGetPreparedQuery’
insertDescriptor: no visible global function definition for
  ‘dbGetPreparedQuery’
insertDescriptorType: no visible global function definition for
  ‘dbGetPreparedQuery’
insertFeature: no visible global function definition for
  ‘dbGetPreparedQuery’
insertNamedDef: no visible global function definition for
  ‘dbGetPreparedQuery’
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’
updatePriorities: no visible global function definition for
  ‘dbGetPreparedQuery’
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 dbGetPreparedQuery 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 ... [43s/67s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
addNewFeatures 3.672  0.189   5.229
loadSdf        2.846  0.039   6.129
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [21s/30s]
 [21s/30s] 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-3.3-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-3.3-bioc/meat/ChemmineR.Rcheck/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘ChemmineR’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘ChemmineR’
Creating a generic function for ‘print’ from package ‘base’ in package ‘ChemmineR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChemmineR)

name	user	system	elapsed
AP-class	0.507	0.077	0.921
APset-class	0.398	0.064	0.464
ExtSDF-class	0.001	0.001	0.001
FP-class	0.090	0.002	0.095
FPset-class	0.419	0.029	0.448
SDF-class	0.086	0.007	0.094
SDF2apcmp	0.024	0.001	0.024
SDFset-class	0.539	0.032	0.575
SDFset2SDF	0.139	0.007	0.146
SDFset2list	0.073	0.031	0.104
SDFstr-class	0.384	0.004	0.390
SMI-class	0.004	0.001	0.006
SMIset-class	0.007	0.002	0.008
addDescriptorType	0.001	0.000	0.001
addNewFeatures	3.672	0.189	5.229
ap	0.122	0.012	0.134
apfp	0.004	0.001	0.005
apset	0.006	0.001	0.006
apset2descdb	0.406	0.067	0.546
atomblock	0.124	0.013	0.137
atomcount	0.245	0.005	0.330
atomprop	0.006	0.001	0.008
atomsubset	0.031	0.002	0.033
batchByIndex	0.001	0.000	0.001
bondblock	0.188	0.012	0.202
bonds	0.039	0.002	0.041
browseJob	0.001	0.001	0.001
bufferLines	0.001	0.000	0.001
bufferResultSet	0.002	0.000	0.002
byCluster	0.792	0.051	0.843
canonicalNumbering	0.800	0.043	1.597
canonicalize	0.048	0.001	0.070
cid	0.026	0.000	0.026
cluster.sizestat	0.585	0.025	0.611
cluster.visualize	0.819	0.015	0.852
cmp.cluster	2.422	0.035	2.548
cmp.duplicated	0.062	0.001	0.064
cmp.parse	0.031	0.001	0.032
cmp.parse1	0.001	0.000	0.001
cmp.search	0.800	0.026	0.942
cmp.similarity	0.027	0.001	0.029
conMA	0.077	0.011	0.088
connections	0.259	0.005	0.356
datablock	0.314	0.008	0.323
datablock2ma	0.048	0.002	0.051
db.explain	0.070	0.006	0.076
db.subset	0.004	0.001	0.005
dbTransaction	0.053	0.007	0.061
desc2fp	0.103	0.003	0.106
draw_sdf	0.576	0.037	0.837
exactMassOB	0.879	0.005	0.885
findCompounds	3.025	0.030	3.069
findCompoundsByName	0.416	0.012	0.430
fingerprintOB	0.001	0.000	0.001
fold	0.002	0.000	0.002
foldCount	0.002	0.000	0.002
fp2bit	0.645	0.015	0.662
fpSim	0.456	0.006	0.468
fptype	0.002	0.000	0.002
fromNNMatrix	1.023	0.002	1.028
genAPDescriptors	0.021	0.001	0.022
genParameters	0.768	0.003	0.781
generate3DCoords	0.000	0.000	0.001
getAllCompoundIds	0.362	0.012	0.723
getCompoundFeatures	2.543	0.032	3.738
getCompoundNames	0.401	0.013	1.375
getCompounds	0.301	0.012	1.341
getIds	0.000	0.000	0.001
grepSDFset	0.055	0.001	0.064
groups	0.173	0.005	0.263
header	0.119	0.002	0.144
initDb	0.042	0.008	1.061
jarvisPatrick	2.597	0.027	3.252
jobToken-class	0.002	0.000	0.002
launchCMTool	0.001	0.000	0.001
listCMTools	0.000	0.000	0.001
listFeatures	0.390	0.012	1.919
loadSdf	2.846	0.039	6.129
makeUnique	0.019	0.001	0.026
maximallyDissimilar	0.221	0.001	0.224
nearestNeighbors	0.955	0.003	0.964
numBits	0.001	0.000	0.002
obmol	0.031	0.002	0.049
parBatchByIndex	0.000	0.000	0.001
plotStruc	0.287	0.006	0.442
propOB	0.001	0.001	0.011
pubchemFPencoding	0.003	0.000	0.021
read.AP	0.095	0.000	0.111
read.SDFindex	0.017	0.001	0.054
read.SDFset	0.640	0.002	0.810
read.SDFstr	0.882	0.003	0.894
read.SMIset	0.002	0.001	0.018
regenerateCoords	0.000	0.000	0.001
result	0.001	0.001	0.001
rings	0.494	0.007	0.565
sdf.subset	0.000	0.000	0.001
sdf.visualize	0.015	0.001	0.024
sdf2ap	0.407	0.063	1.898
sdf2list	0.026	0.008	0.391
sdf2smiles	0.001	0.000	0.525
sdf2str	0.041	0.004	0.320
sdfStream	0.017	0.001	0.024
sdfid	0.021	0.001	0.084
sdfsample	0.053	0.002	0.069
sdfstr2list	1.366	0.304	4.509
searchSim	0.001	0.001	0.001
searchString	0.000	0.000	0.001
selectInBatches	0.002	0.000	0.002
setPriorities	0.001	0.000	0.001
smartsSearchOB	0.001	0.000	0.002
smiles2sdf	0.001	0.000	0.000
smisample	0.005	0.001	0.005
status	0.001	0.000	0.001
toolDetails	0.001	0.000	0.001
trimNeighbors	1.952	0.006	1.963
validSDF	0.027	0.001	0.029
view	0.081	0.004	0.086
write.SDF	0.256	0.004	0.260
write.SDFsplit	0.020	0.000	0.021
write.SMI	0.003	0.000	0.003