BioC 2.13: CHECK report for ChemmineR on zin1

Package: ChemmineR

Version: 2.14.3

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.14.3.tar.gz

StartedAt: 2014-04-05 00:10:31 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:12:23 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 111.6 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ChemmineR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-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 ‘2.14.3’
* 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 ... [8s/8s] 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:
  ‘methods’
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
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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’
fingerprintOB: no visible global function definition for
  ‘fingerprint_OB’
propOB: no visible global function definition for ‘prop_OB’
sdf2smiles: no visible global function definition for ‘convertFormat’
sdf2smilesOB: no visible global function definition for ‘convertFormat’
smile2sdfFile: no visible global function definition for
  ‘convertFormatFile’
smiles2sdf: no visible global function definition for ‘convertFormat’
smiles2sdfOB: no visible global function definition for ‘convertFormat’
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.13-bioc/meat/ChemmineR.Rcheck/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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ChemmineR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [44s/44s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
jarvisPatrick 4.852  0.248   5.188
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [19s/20s]
 [19s/20s] 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

NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c DisjointSets.cpp -o DisjointSets.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/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]
cluster.cc:118:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function ‘int contains(int, std::vector<int>&)’:
cluster.cc:131:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXP)’:
cluster.cc:284:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc:298:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc: In function ‘void loadNNList(int, int, SEXP)’:
cluster.cc:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cluster.cc:332:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
cluster.cc: At global scope:
cluster.cc:49:13: warning: ‘void prepare_neighbors(const char*, int, int)’ defined but not used [-Wunused-function]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXP)’:
desc.cc:202:7: warning: unused variable ‘id’ [-Wunused-variable]
desc.cc:253:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
desc.cc:180:6: warning: unused variable ‘d’ [-Wunused-variable]
desc.cc:218:6: warning: unused variable ‘Rf_ncols’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c formats.cc -o formats.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c molecule.cc -o molecule.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/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:943:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c script.cc -o script.o
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c similarity.cc -o similarity.o
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
g++ -shared -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o desc.o formats.o molecule.o r_wrap.o script.o similarity.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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	0.712	0.048	0.783
APset-class	0.688	0.044	0.758
FP-class	0.132	0.008	0.141
FPset-class	0.504	0.000	0.505
SDF-class	0.064	0.004	0.071
SDF2apcmp	0.028	0.000	0.029
SDFset-class	0.528	0.020	0.548
SDFset2SDF	0.184	0.004	0.188
SDFset2list	0.068	0.012	0.082
SDFstr-class	0.344	0.000	0.347
SMI-class	0.008	0.000	0.009
SMIset-class	0.012	0.008	0.019
addNewFeatures	3.100	0.016	3.122
ap	0.324	0.004	0.330
apfp	0.008	0.000	0.006
apset	0.012	0.000	0.011
apset2descdb	0.684	0.040	0.725
atomblock	0.256	0.016	0.272
atomcount	0.308	0.000	0.310
atomprop	0.004	0.000	0.007
atomsubset	0.084	0.004	0.087
batchByIndex	0.004	0.000	0.005
bondblock	0.192	0.004	0.197
bonds	0.040	0.004	0.043
bufferLines	0.000	0.004	0.003
bufferResultSet	0.000	0.000	0.004
byCluster	1.060	0.000	1.063
cid	0.056	0.004	0.059
cluster.sizestat	0.624	0.012	0.639
cluster.visualize	0.776	0.008	0.786
cmp.cluster	2.464	0.008	2.477
cmp.duplicated	0.068	0.008	0.075
cmp.parse	0.028	0.004	0.033
cmp.parse1	0.004	0.000	0.003
cmp.search	0.804	0.008	0.815
cmp.similarity	0.024	0.004	0.027
conMA	0.068	0.004	0.073
datablock	0.444	0.008	0.452
datablock2ma	0.096	0.000	0.097
db.explain	0.052	0.004	0.058
db.subset	0.008	0.000	0.009
dbTransaction	0.036	0.008	0.045
desc2fp	0.168	0.004	0.172
findCompounds	2.865	0.012	2.933
findCompoundsByName	0.516	0.000	0.548
fingerprintOB	0.004	0.000	0.003
fp2bit	0.888	0.016	0.905
fpSim	0.940	0.004	0.948
fromNNMatrix	1.080	0.004	1.088
genAPDescriptors	0.024	0.000	0.024
getCompoundNames	0.460	0.004	0.464
getCompounds	0.468	0.012	0.479
getIds	0.004	0.000	0.004
grepSDFset	0.072	0.000	0.073
groups	0.168	0.012	0.179
header	0.140	0.000	0.142
initDb	0.048	0.004	0.050
jarvisPatrick	4.852	0.248	5.188
listFeatures	0.588	0.028	0.615
loadSdf	3.309	0.116	3.433
makeUnique	0.076	0.012	0.089
nearestNeighbors	1.824	0.084	1.916
parBatchByIndex	0.004	0.000	0.004
plotStruc	0.320	0.048	0.368
propOB	0.000	0.000	0.002
pubchemFPencoding	0.004	0.000	0.007
read.AP	0.028	0.000	0.027
read.SDFindex	0.028	0.000	0.025
read.SDFset	0.772	0.044	0.822
read.SDFstr	1.132	0.012	1.147
read.SMIset	0.012	0.000	0.010
rings	0.704	0.008	0.726
sdf.subset	0.000	0.000	0.004
sdf.visualize	0.020	0.000	0.022
sdf2ap	0.608	0.040	0.677
sdf2list	0.024	0.008	0.034
sdf2smiles	0.004	0.000	0.003
sdf2str	0.040	0.000	0.039
sdfStream	0.028	0.000	0.028
sdfid	0.036	0.000	0.038
sdfsample	0.060	0.004	0.065
sdfstr2list	0.752	0.188	0.964
searchSim	0.004	0.000	0.004
searchString	0.004	0.000	0.003
selectInBatches	0.008	0.000	0.008
smiles2sdf	0.000	0.000	0.004
smisample	0.008	0.000	0.007
trimNeighbors	2.504	0.000	2.549
validSDF	0.040	0.000	0.044
view	0.132	0.004	0.135
write.SDF	0.252	0.004	0.259
write.SDFsplit	0.076	0.000	0.075
write.SMI	0.004	0.000	0.005