BioC 2.14: CHECK report for ChemmineR on morelia

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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-darwin13.1.0 (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 ... [9s/10s] 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 ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
  -stdlib=libstdc++
* 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 ... [45s/46s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [22s/23s]
 [22s/24s] 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

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c DisjointSets.cpp -o DisjointSets.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c cluster.cc -o cluster.o
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
            ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c desc.cc -o desc.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c formats.cc -o formats.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c molecule.cc -o molecule.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c r_wrap.cc -o r_wrap.o
r_wrap.cc:1689:14: warning: explicitly assigning a variable of type 'void *' to itself [-Wself-assign]
  clientdata = clientdata;
  ˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c script.cc -o script.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c similarity.cc -o similarity.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o desc.o formats.o molecule.o r_wrap.o script.o similarity.o -stdlib=libstdc++ -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	0.797	0.070	0.868
APset-class	0.690	0.071	0.762
FP-class	0.093	0.002	0.095
FPset-class	0.430	0.023	0.454
SDF-class	0.074	0.007	0.080
SDF2apcmp	0.076	0.001	0.077
SDFset-class	0.551	0.029	0.581
SDFset2SDF	0.172	0.008	0.181
SDFset2list	0.088	0.031	0.120
SDFstr-class	0.497	0.004	0.502
SMI-class	0.003	0.000	0.004
SMIset-class	0.009	0.001	0.010
addDescriptorType	0.001	0.001	0.001
addNewFeatures	3.596	0.112	3.807
ap	0.406	0.015	0.421
apfp	0.003	0.000	0.004
apset	0.005	0.001	0.006
apset2descdb	0.672	0.064	0.736
atomblock	0.135	0.013	0.149
atomcount	0.303	0.004	0.308
atomprop	0.005	0.001	0.005
atomsubset	0.036	0.001	0.037
batchByIndex	0.001	0.001	0.001
bondblock	0.130	0.008	0.138
bonds	0.035	0.003	0.037
bufferLines	0.001	0.000	0.001
bufferResultSet	0.002	0.001	0.002
byCluster	0.937	0.005	0.943
cid	0.052	0.001	0.053
cluster.sizestat	0.589	0.005	0.594
cluster.visualize	0.834	0.008	0.842
cmp.cluster	2.163	0.019	2.182
cmp.duplicated	0.054	0.001	0.055
cmp.parse	0.029	0.001	0.030
cmp.parse1	0.001	0.000	0.000
cmp.search	0.788	0.009	0.798
cmp.similarity	0.023	0.001	0.024
conMA	0.075	0.008	0.084
datablock	0.470	0.008	0.478
datablock2ma	0.054	0.001	0.056
db.explain	0.078	0.006	0.084
db.subset	0.005	0.001	0.005
dbTransaction	0.065	0.006	0.072
desc2fp	0.192	0.003	0.196
findCompounds	2.837	0.028	2.868
findCompoundsByName	0.591	0.011	0.622
fingerprintOB	0.000	0.000	0.001
fold	0.002	0.000	0.002
foldCount	0.002	0.000	0.002
fp2bit	0.945	0.013	0.958
fpSim	1.027	0.014	1.045
fptype	0.001	0.000	0.001
fromNNMatrix	0.957	0.015	0.974
genAPDescriptors	0.027	0.001	0.029
getCompoundNames	0.488	0.015	0.504
getCompounds	0.484	0.011	0.496
getIds	0.000	0.000	0.001
grepSDFset	0.131	0.001	0.133
groups	0.150	0.003	0.153
header	0.133	0.002	0.136
initDb	0.052	0.006	0.059
jarvisPatrick	3.841	0.022	3.866
listFeatures	0.569	0.013	0.583
loadSdf	3.391	0.034	3.432
makeUnique	0.023	0.001	0.024
maximallyDissimilar	0.425	0.001	0.435
nearestNeighbors	1.771	0.032	1.804
numBits	0.001	0.000	0.002
obmol	0.977	0.028	1.041
parBatchByIndex	0.001	0.001	0.001
plotStruc	0.364	0.006	0.371
propOB	0.000	0.000	0.001
pubchemFPencoding	0.004	0.001	0.005
read.AP	0.020	0.000	0.021
read.SDFindex	0.017	0.000	0.018
read.SDFset	0.867	0.002	0.869
read.SDFstr	1.252	0.003	1.254
read.SMIset	0.002	0.000	0.002
regenerateCoords	0	0	0
rings	0.634	0.008	0.642
sdf.subset	0.000	0.000	0.001
sdf.visualize	0.019	0.001	0.019
sdf2ap	0.691	0.068	0.761
sdf2list	0.028	0.008	0.036
sdf2smiles	0.000	0.000	0.001
sdf2str	0.038	0.003	0.040
sdfStream	0.025	0.001	0.026
sdfid	0.024	0.001	0.025
sdfsample	0.063	0.003	0.066
sdfstr2list	1.547	0.309	1.859
searchSim	0.001	0.000	0.000
searchString	0.001	0.000	0.001
selectInBatches	0.001	0.001	0.001
setPriorities	0.001	0.000	0.001
smartsSearchOB	0.001	0.000	0.001
smiles2sdf	0.001	0.001	0.000
smisample	0.005	0.000	0.005
trimNeighbors	2.420	0.013	2.435
validSDF	0.029	0.000	0.029
view	0.119	0.003	0.123
write.SDF	0.251	0.003	0.253
write.SDFsplit	0.017	0.000	0.017
write.SMI	0.002	0.001	0.003

BioC 2.14: CHECK report for ChemmineR on morelia

Summary

Command output