BioC 2.14: CHECK report for ChemmineR on zin2

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.16.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/ChemmineR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.16.9’
* 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 ... [8s/8s] 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 ‘/home/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 ... [38s/39s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [19s/20s]
 [20s/20s] 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
  ‘/home/biocbuild/bbs-2.14-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.14-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-2.14-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-2.14-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:249:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-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-2.14-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-2.14-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:949:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.14-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-2.14-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-2.14-bioc/R/lib -lR
installing to /home/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	0.760	0.048	0.809
APset-class	0.544	0.060	0.603
FP-class	0.096	0.000	0.095
FPset-class	0.396	0.008	0.405
SDF-class	0.060	0.004	0.065
SDF2apcmp	0.072	0.000	0.070
SDFset-class	0.428	0.016	0.446
SDFset2SDF	0.144	0.008	0.150
SDFset2list	0.064	0.024	0.086
SDFstr-class	0.408	0.000	0.408
SMI-class	0.004	0.000	0.003
SMIset-class	0.008	0.000	0.009
addDescriptorType	0	0	0
addNewFeatures	3.084	0.040	3.128
ap	0.336	0.004	0.339
apfp	0.004	0.000	0.003
apset	0.008	0.000	0.006
apset2descdb	0.584	0.056	0.641
atomblock	0.120	0.004	0.126
atomcount	0.240	0.004	0.245
atomprop	0.004	0.000	0.005
atomsubset	0.036	0.000	0.033
batchByIndex	0.000	0.000	0.001
bondblock	0.120	0.008	0.131
bonds	0.032	0.004	0.037
bufferLines	0	0	0
bufferResultSet	0.004	0.000	0.001
byCluster	1.020	0.004	1.027
cid	0.048	0.000	0.049
cluster.sizestat	0.604	0.004	0.610
cluster.visualize	0.788	0.000	0.792
cmp.cluster	2.208	0.024	2.236
cmp.duplicated	0.064	0.000	0.066
cmp.parse	0.028	0.000	0.028
cmp.parse1	0	0	0
cmp.search	0.800	0.008	0.810
cmp.similarity	0.020	0.000	0.023
conMA	0.064	0.004	0.064
datablock	0.308	0.000	0.308
datablock2ma	0.036	0.000	0.038
db.explain	0.052	0.000	0.053
db.subset	0.000	0.004	0.004
dbTransaction	0.036	0.004	0.037
desc2fp	0.168	0.000	0.167
findCompounds	2.573	0.008	2.583
findCompoundsByName	0.408	0.004	0.415
fingerprintOB	0.000	0.000	0.001
fold	0.004	0.000	0.002
foldCount	0.000	0.000	0.001
fp2bit	0.792	0.036	0.830
fpSim	0.836	0.024	0.861
fptype	0.004	0.000	0.002
fromNNMatrix	0.956	0.000	0.959
genAPDescriptors	0.020	0.000	0.021
getCompoundNames	0.388	0.012	0.399
getCompounds	0.404	0.008	0.410
getIds	0	0	0
grepSDFset	0.052	0.000	0.075
groups	0.136	0.000	0.137
header	0.108	0.004	0.112
initDb	0.036	0.000	0.036
jarvisPatrick	3.840	0.084	3.952
listFeatures	0.432	0.004	0.434
loadSdf	2.852	0.008	2.895
makeUnique	0.020	0.000	0.019
maximallyDissimilar	0.4	0.0	0.4
nearestNeighbors	1.528	0.004	1.534
numBits	0.000	0.000	0.002
obmol	0.272	0.024	0.472
parBatchByIndex	0.004	0.000	0.001
plotStruc	0.292	0.004	0.324
propOB	0.004	0.000	0.001
pubchemFPencoding	0.004	0.000	0.004
read.AP	0.020	0.000	0.021
read.SDFindex	0.016	0.000	0.019
read.SDFset	0.748	0.004	0.759
read.SDFstr	1.045	0.000	1.045
read.SMIset	0.004	0.000	0.002
regenerateCoords	0.000	0.000	0.001
rings	0.604	0.000	0.606
sdf.subset	0.004	0.000	0.000
sdf.visualize	0.016	0.000	0.016
sdf2ap	0.576	0.020	0.598
sdf2list	0.024	0.004	0.027
sdf2smiles	0.004	0.000	0.000
sdf2str	0.028	0.000	0.031
sdfStream	0.016	0.000	0.017
sdfid	0.020	0.000	0.019
sdfsample	0.052	0.004	0.055
sdfstr2list	0.768	0.160	0.929
searchSim	0.000	0.000	0.001
searchString	0	0	0
selectInBatches	0.004	0.000	0.002
setPriorities	0	0	0
smartsSearchOB	0.000	0.000	0.001
smiles2sdf	0	0	0
smisample	0.004	0.000	0.004
trimNeighbors	2.216	0.000	2.221
validSDF	0.024	0.000	0.024
view	0.120	0.004	0.122
write.SDF	0.232	0.008	0.239
write.SDFsplit	0.016	0.000	0.018
write.SMI	0.000	0.000	0.002

BioC 2.14: CHECK report for ChemmineR on zin2

Summary

Command output