BioC 3.3: CHECK report for ChemmineR on zin2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.24.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ChemmineR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.24.2’
* 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’
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 ... 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’ ... 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: 5 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  -Wall -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  -Wall -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int>&, std::vector<int>&)’:
cluster.cc:118:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
                        ^
cluster.cc:118:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
                                             ^
cluster.cc: In function ‘int contains(int, std::vector<int>&)’:
cluster.cc:131:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < list.size(); i++)
                             ^
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j = 0; j < nbr_list[i].size(); j ++) {
                                        ^
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXP)’:
cluster.cc:284:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                      ^
cluster.cc:298:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(nbrs.size() < minNbrs) // will end up a singleton
                    ^
cluster.cc: In function ‘void loadNNList(int, int, SEXP)’:
cluster.cc:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                      ^
cluster.cc:332:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(nbrs.size() < minNbrs) // will end up a singleton
                    ^
cluster.cc: In function ‘SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)’:
cluster.cc:390:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++){
                      ^
cluster.cc: At global scope:
cluster.cc:49:13: warning: ‘void prepare_neighbors(const char*, int, int)’ defined but not used [-Wunused-function]
 void static prepare_neighbors(const char* nbr_file, int skip, int p)
             ^
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  -Wall -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  -Wall -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXP)’:
desc.cc:249:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < descs.size(); i++)
                              ^
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  -Wall -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function ‘SEXPREC* uniquifyAtomPairs(SEXP)’:
fingerprints.cc:138:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++)
                            ^
fingerprints.cc:145:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
                            ^
fingerprints.cc:158:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
                            ^
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  -Wall -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  -Wall -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  -Wall -c r_wrap.cc -o r_wrap.o
r_wrap.cc: In function ‘SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)’:
r_wrap.cc:949:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
   const char *p = typeName;
               ^
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  -Wall -c script.cc -o script.o
In file included from script.cc:2:0:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
 static char elements[112][3] = {
             ^
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  -Wall -c similarity.cc -o similarity.o
In file included from similarity.cc:1:0:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
 static char elements[112][3] = {
             ^
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.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	0.415	0.028	0.442
APset-class	0.297	0.060	0.358
ExtSDF-class	0.001	0.000	0.001
FP-class	0.088	0.000	0.088
FPset-class	0.353	0.008	0.360
SDF-class	0.055	0.004	0.059
SDF2apcmp	0.028	0.000	0.027
SDFset-class	0.307	0.024	0.331
SDFset2SDF	0.102	0.000	0.102
SDFset2list	0.046	0.016	0.062
SDFstr-class	0.265	0.004	0.273
SMI-class	0.003	0.000	0.003
SMIset-class	0.007	0.000	0.006
addDescriptorType	0.000	0.000	0.001
addNewFeatures	2.747	0.015	2.789
ap	0.084	0.008	0.097
apfp	0.002	0.004	0.003
apset	0.002	0.000	0.005
apset2descdb	0.323	0.036	0.361
atomblock	0.079	0.012	0.092
atomcount	0.209	0.012	0.224
atomprop	0.003	0.000	0.004
atomsubset	0.026	0.000	0.028
batchByIndex	0.000	0.000	0.001
bondblock	0.081	0.000	0.083
bonds	0.029	0.000	0.029
browseJob	0.001	0.000	0.001
bufferLines	0	0	0
bufferResultSet	0.001	0.000	0.001
byCluster	0.804	0.000	0.822
canonicalNumbering	0.186	0.019	0.698
canonicalize	0.034	0.000	0.037
cid	0.02	0.00	0.02
cluster.sizestat	0.600	0.000	0.619
cluster.visualize	0.737	0.008	0.757
cmp.cluster	2.243	0.013	2.259
cmp.duplicated	0.073	0.000	0.072
cmp.parse	0.026	0.000	0.025
cmp.parse1	0.000	0.000	0.001
cmp.search	0.752	0.004	0.758
cmp.similarity	0.024	0.000	0.023
conMA	0.056	0.008	0.064
connections	0.166	0.000	0.613
datablock	0.233	0.008	0.243
datablock2ma	0.036	0.000	0.036
db.explain	0.047	0.004	0.052
db.subset	0.004	0.000	0.004
dbTransaction	0.024	0.008	0.033
desc2fp	0.116	0.004	0.122
draw_sdf	0.379	0.019	0.439
exactMassOB	0.586	0.000	0.594
findCompounds	2.269	0.003	2.338
findCompoundsByName	0.301	0.000	0.302
fingerprintOB	0.001	0.000	0.001
fold	0.002	0.000	0.001
foldCount	0.001	0.000	0.001
fp2bit	0.466	0.008	0.474
fpSim	0.286	0.000	0.286
fptype	0.001	0.000	0.001
fromNNMatrix	0.942	0.000	0.943
genAPDescriptors	0.019	0.000	0.019
genParameters	0.667	0.000	0.667
generate3DCoords	0.000	0.000	0.001
getAllCompoundIds	0.329	0.008	0.337
getCompoundFeatures	2.178	0.008	2.191
getCompoundNames	0.325	0.004	0.329
getCompounds	0.458	0.008	0.466
getIds	0	0	0
grepSDFset	0.045	0.004	0.049
groups	0.119	0.004	0.123
header	0.081	0.000	0.082
initDb	0.025	0.000	0.025
jarvisPatrick	1.938	0.004	1.949
jobToken-class	0.001	0.000	0.001
launchCMTool	0.001	0.000	0.001
listCMTools	0.000	0.000	0.001
listFeatures	0.352	0.004	0.364
loadSdf	2.436	0.008	2.482
makeUnique	0.019	0.000	0.019
maximallyDissimilar	0.255	0.000	0.255
nearestNeighbors	1.238	0.008	1.247
numBits	0.001	0.000	0.001
obmol	0.033	0.000	0.036
parBatchByIndex	0.001	0.000	0.001
plotStruc	0.265	0.000	0.265
propOB	0	0	0
pubchemFPencoding	0.000	0.000	0.003
read.AP	0.015	0.000	0.018
read.SDFindex	0.018	0.000	0.018
read.SDFset	0.668	0.004	0.675
read.SDFstr	1.013	0.000	1.019
read.SMIset	0.002	0.000	0.002
regenerateCoords	0	0	0
result	0.001	0.000	0.001
rings	0.486	0.004	0.490
sdf.subset	0	0	0
sdf.visualize	0.018	0.000	0.019
sdf2ap	0.369	0.040	0.415
sdf2list	0.032	0.000	0.035
sdf2smiles	0.001	0.000	0.000
sdf2str	0.027	0.004	0.031
sdfStream	0.019	0.000	0.019
sdfid	0.02	0.00	0.02
sdfsample	0.053	0.000	0.053
sdfstr2list	0.716	0.183	0.905
searchSim	0.001	0.000	0.001
searchString	0	0	0
selectInBatches	0.001	0.000	0.001
setPriorities	0.001	0.000	0.001
smartsSearchOB	0	0	0
smiles2sdf	0.000	0.004	0.001
smisample	0.001	0.000	0.004
status	0.001	0.000	0.000
toolDetails	0.000	0.000	0.001
trimNeighbors	1.752	0.012	1.780
validSDF	0.017	0.004	0.022
view	0.054	0.000	0.054
write.SDF	0.158	0.004	0.161
write.SDFsplit	0.018	0.000	0.018
write.SMI	0.002	0.000	0.002

BioC 3.3: CHECK report for ChemmineR on zin2

Summary

Command output