BioC 3.3: CHECK report for ChemmineR on linux2.bioconductor.org

Package: ChemmineR

Version: 2.23.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.23.0.tar.gz

StartedAt: 2015-10-27 02:25:14 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:27:07 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 112.9 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ChemmineR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘2.23.0’
* 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/18s] 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 binding for global variable ‘string’
.parseV3000: no visible binding for global variable ‘AW’
applyOptions: no visible global function definition for ‘convertFormat’
canonicalNumbering: no visible global function definition for
  ‘canonicalNumbering_OB’
canonicalNumberingOB: no visible global function definition for
  ‘canonicalNumbering_OB’
concatenate_plots: no visible binding for global variable ‘arrangeGrob’
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’
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’
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’
sdf2OBMol: no visible global function definition for ‘forEachMol’
sdf2smiles: no visible global function definition for ‘convertFormat’
sdf2smilesOB: no visible global function definition for ‘convertFormat’
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’
Undefined global functions or variables:
  AW C1 C1.1 C2 C2.1 arrangeGrob canonicalNumbering_OB clusterApplyLB
  clusterExport convertFormat convertFormatFile dbGetPreparedQuery
  error exactMass_OB fingerprint_OB fmcs forEachMol
  postgresqlCopyInDataframe postgresqlQuoteId postgresqlTableRef
  postgresqlgetResult postgresqlpqExec prop_OB rasterGrob readPNG
  smartsSearch_OB string
* 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 ... 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... [34s/34s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [14s/15s]
 [15s/15s] 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: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -c DisjointSets.cpp -o DisjointSets.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -c cluster.cc -o cluster.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -c cstrsplit.cc -o cstrsplit.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -c desc.cc -o desc.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -c fingerprints.cc -o fingerprints.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -c formats.cc -o formats.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -c molecule.cc -o molecule.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -c r_wrap.cc -o r_wrap.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -c script.cc -o script.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -c similarity.cc -o similarity.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/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 -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/ChemmineR.Rcheck/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘as.vector’ from package ‘base’ in package ‘ChemmineR’
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	0.440	0.076	0.516
APset-class	0.451	0.036	0.487
ExtSDF-class	0.002	0.000	0.001
FP-class	0.101	0.000	0.102
FPset-class	0.314	0.012	0.327
SDF-class	0.047	0.008	0.055
SDF2apcmp	0.032	0.000	0.032
SDFset-class	0.495	0.028	0.525
SDFset2SDF	0.153	0.000	0.153
SDFset2list	0.073	0.012	0.085
SDFstr-class	0.372	0.008	0.380
SMI-class	0.004	0.000	0.004
SMIset-class	0.007	0.000	0.008
addDescriptorType	0	0	0
addNewFeatures	2.087	0.023	2.118
ap	0.070	0.008	0.078
apfp	0.002	0.000	0.002
apset	0.004	0.000	0.003
apset2descdb	0.261	0.044	0.305
atomblock	0.072	0.008	0.081
atomcount	0.156	0.000	0.156
atomprop	0.003	0.000	0.003
atomsubset	0.023	0.000	0.023
batchByIndex	0	0	0
bondblock	0.075	0.004	0.080
bonds	0.027	0.000	0.027
browseJob	0.001	0.000	0.000
bufferLines	0.000	0.000	0.001
bufferResultSet	0.001	0.000	0.001
byCluster	0.806	0.000	0.806
canonicalNumbering	0.183	0.008	0.261
canonicalize	0.03	0.00	0.03
cid	0.018	0.000	0.018
cluster.sizestat	0.480	0.004	0.485
cluster.visualize	0.597	0.000	0.599
cmp.cluster	2.024	0.012	2.039
cmp.duplicated	0.056	0.000	0.056
cmp.parse	0.021	0.000	0.022
cmp.parse1	0.001	0.000	0.000
cmp.search	0.702	0.008	0.710
cmp.similarity	0.016	0.000	0.016
conMA	0.047	0.004	0.051
connections	0.160	0.000	0.168
datablock	0.21	0.00	0.21
datablock2ma	0.028	0.000	0.028
db.explain	0.037	0.000	0.037
db.subset	0.004	0.000	0.003
dbTransaction	0.024	0.000	0.024
desc2fp	0.09	0.00	0.09
draw_sdf	0.276	0.012	0.289
exactMassOB	0.479	0.000	0.479
findCompounds	2.522	0.000	2.523
findCompoundsByName	0.557	0.004	0.562
fingerprintOB	0.000	0.000	0.001
fold	0.001	0.000	0.002
foldCount	0.001	0.000	0.002
fp2bit	0.497	0.004	0.501
fpSim	0.409	0.004	0.414
fptype	0.001	0.000	0.002
fromNNMatrix	0.921	0.000	0.920
genAPDescriptors	0.015	0.000	0.015
genParameters	0.485	0.004	0.489
generate3DCoords	0.001	0.000	0.000
getAllCompoundIds	0.257	0.004	0.261
getCompoundFeatures	2.334	0.004	2.339
getCompoundNames	0.442	0.008	0.450
getCompounds	0.461	0.000	0.461
getIds	0	0	0
grepSDFset	0.044	0.000	0.044
groups	0.090	0.004	0.094
header	0.078	0.000	0.078
initDb	0.021	0.000	0.021
jarvisPatrick	1.892	0.000	1.892
jobToken-class	0.000	0.000	0.001
launchCMTool	0.001	0.000	0.000
listCMTools	0.001	0.000	0.001
listFeatures	0.281	0.008	0.289
loadSdf	2.069	0.004	2.073
makeUnique	0.015	0.000	0.015
maximallyDissimilar	0.217	0.000	0.217
nearestNeighbors	1.048	0.000	1.048
numBits	0.001	0.000	0.001
obmol	0.026	0.000	0.026
parBatchByIndex	0.001	0.000	0.001
plotStruc	0.284	0.008	0.292
propOB	0.001	0.000	0.001
pubchemFPencoding	0.002	0.000	0.002
read.AP	0.014	0.000	0.014
read.SDFindex	0.014	0.000	0.014
read.SDFset	0.52	0.00	0.52
read.SDFstr	0.723	0.000	0.723
read.SMIset	0.001	0.000	0.001
regenerateCoords	0.001	0.000	0.001
result	0.001	0.000	0.001
rings	0.348	0.008	0.356
sdf.subset	0	0	0
sdf.visualize	0.014	0.000	0.014
sdf2ap	0.290	0.032	0.322
sdf2list	0.023	0.000	0.023
sdf2smiles	0	0	0
sdf2str	0.021	0.004	0.025
sdfStream	0.021	0.000	0.021
sdfid	0.027	0.000	0.027
sdfsample	0.074	0.000	0.074
sdfstr2list	0.964	0.276	1.239
searchSim	0.001	0.000	0.001
searchString	0.001	0.000	0.001
selectInBatches	0.002	0.000	0.002
setPriorities	0.001	0.000	0.001
smartsSearchOB	0.001	0.000	0.001
smiles2sdf	0.001	0.000	0.000
smisample	0.004	0.000	0.004
status	0.001	0.000	0.001
toolDetails	0.001	0.000	0.001
trimNeighbors	2.199	0.000	2.199
validSDF	0.019	0.000	0.020
view	0.045	0.000	0.046
write.SDF	0.25	0.00	0.25
write.SDFsplit	0.024	0.000	0.024
write.SMI	0.003	0.000	0.003