BioC 2.14: CHECK report for ChemmineR on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.16.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/ChemmineR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.16.9’
* 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 ... [17s/18s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘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
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))

Error in validObject(.Object) : 
  invalid class “ObjectsWithPackage” object: superclass "EnumerationValue" not defined in the environment of the object's class
Calls: <Anonymous> ... metaNameUndo -> new -> initialize -> initialize -> validObject
Execution halted
* 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 ‘/Users/biocbuild/bbs-2.14-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 files in ‘vignettes’ ... OK
* checking examples ... [82s/83s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
jarvisPatrick  7.494  0.033   7.543
addNewFeatures 6.529  0.200   6.972
loadSdf        6.264  0.075   6.451
findCompounds  5.454  0.055   5.551
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [39s/43s]
 [40s/43s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘RefManageR’
* 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
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c DisjointSets.cpp -o DisjointSets.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&)’:
cluster.cc:118: warning: comparison between signed and unsigned integer expressions
cluster.cc:118: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘int contains(int, std::vector<int, std::allocator<int> >&)’:
cluster.cc:131: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXPREC*)’:
cluster.cc:284: warning: comparison between signed and unsigned integer expressions
cluster.cc:298: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘void loadNNList(int, int, SEXPREC*)’:
cluster.cc:314: warning: comparison between signed and unsigned integer expressions
cluster.cc:332: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘SEXPREC* jarvis_patrick(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
cluster.cc:390: warning: comparison between signed and unsigned integer expressions
cluster.cc: At global scope:
cluster.cc:49: warning: ‘void prepare_neighbors(const char*, int, int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXPREC*)’:
desc.cc:249: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c formats.cc -o formats.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c molecule.cc -o molecule.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c r_wrap.cc -o r_wrap.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c script.cc -o script.o
desc.h:39: warning: ‘elements’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c similarity.cc -o similarity.o
desc.h:39: warning: ‘elements’ defined but not used
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o desc.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-2.14-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	1.382	0.121	1.522
APset-class	1.145	0.118	1.267
FP-class	0.153	0.003	0.156
FPset-class	0.726	0.036	0.763
SDF-class	0.135	0.011	0.146
SDF2apcmp	0.140	0.001	0.142
SDFset-class	0.944	0.050	1.001
SDFset2SDF	0.282	0.013	0.294
SDFset2list	0.150	0.053	0.203
SDFstr-class	0.790	0.010	0.801
SMI-class	0.007	0.001	0.007
SMIset-class	0.016	0.002	0.018
addDescriptorType	0.001	0.000	0.001
addNewFeatures	6.529	0.200	6.972
ap	0.685	0.021	0.707
apfp	0.005	0.001	0.006
apset	0.011	0.002	0.013
apset2descdb	1.220	0.115	1.337
atomblock	0.261	0.025	0.285
atomcount	0.476	0.007	0.484
atomprop	0.008	0.001	0.008
atomsubset	0.060	0.002	0.061
batchByIndex	0.002	0.000	0.002
bondblock	0.258	0.016	0.275
bonds	0.066	0.003	0.070
bufferLines	0.001	0.000	0.001
bufferResultSet	0.003	0.001	0.003
byCluster	1.820	0.007	1.834
cid	0.092	0.002	0.093
cluster.sizestat	1.190	0.008	1.201
cluster.visualize	1.598	0.011	1.614
cmp.cluster	4.459	0.035	4.688
cmp.duplicated	0.087	0.001	0.089
cmp.parse	0.048	0.001	0.051
cmp.parse1	0.002	0.001	0.002
cmp.search	1.501	0.017	1.522
cmp.similarity	0.045	0.002	0.047
conMA	0.122	0.014	0.138
datablock	0.782	0.014	0.797
datablock2ma	0.088	0.003	0.091
db.explain	0.144	0.011	0.155
db.subset	0.007	0.001	0.009
dbTransaction	0.123	0.013	0.155
desc2fp	0.310	0.010	0.319
findCompounds	5.454	0.055	5.551
findCompoundsByName	1.016	0.027	1.059
fingerprintOB	0.001	0.000	0.001
fold	0.004	0.001	0.004
foldCount	0.003	0.000	0.003
fp2bit	1.610	0.026	1.638
fpSim	1.647	0.023	1.674
fptype	0.003	0.000	0.002
fromNNMatrix	1.788	0.007	1.797
genAPDescriptors	0.049	0.001	0.049
getCompoundNames	0.917	0.023	0.957
getCompounds	0.996	0.025	1.036
getIds	0.001	0.000	0.001
grepSDFset	0.114	0.001	0.116
groups	0.283	0.008	0.292
header	0.261	0.005	0.266
initDb	0.127	0.012	0.150
jarvisPatrick	7.494	0.033	7.543
listFeatures	0.975	0.022	1.013
loadSdf	6.264	0.075	6.451
makeUnique	0.042	0.001	0.044
maximallyDissimilar	0.772	0.003	0.776
nearestNeighbors	3.363	0.009	3.392
numBits	0.003	0.000	0.002
obmol	1.472	0.043	1.539
parBatchByIndex	0.002	0.001	0.002
plotStruc	0.722	0.011	0.736
propOB	0.001	0.001	0.001
pubchemFPencoding	0.006	0.000	0.007
read.AP	0.035	0.001	0.036
read.SDFindex	0.034	0.001	0.036
read.SDFset	1.421	0.004	1.428
read.SDFstr	2.199	0.008	2.231
read.SMIset	0.004	0.001	0.005
regenerateCoords	0.001	0.000	0.001
rings	1.234	0.018	1.269
sdf.subset	0.001	0.000	0.002
sdf.visualize	0.035	0.001	0.037
sdf2ap	1.310	0.116	1.429
sdf2list	0.051	0.016	0.067
sdf2smiles	0.001	0.000	0.001
sdf2str	0.070	0.007	0.077
sdfStream	0.040	0.002	0.041
sdfid	0.040	0.001	0.042
sdfsample	0.114	0.005	0.119
sdfstr2list	2.976	0.557	3.604
searchSim	0.002	0.000	0.002
searchString	0.001	0.000	0.002
selectInBatches	0.004	0.001	0.004
setPriorities	0.001	0.000	0.001
smartsSearchOB	0.001	0.000	0.001
smiles2sdf	0.001	0.000	0.002
smisample	0.008	0.001	0.009
trimNeighbors	4.370	0.008	4.389
validSDF	0.047	0.001	0.049
view	0.233	0.006	0.238
write.SDF	0.453	0.009	0.461
write.SDFsplit	0.033	0.002	0.035
write.SMI	0.004	0.000	0.004

BioC 2.14: CHECK report for ChemmineR on petty

Summary

Command output