BioC 2.13: CHECK report for ChemmineR on perceval

Package: ChemmineR

Version: 2.14.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.14.3.tar.gz

StartedAt: 2014-04-05 00:10:48 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:13:31 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 163.0 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ChemmineR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.14.3’
* 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 ... [11s/11s] 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 ‘/Users/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 sizes of PDF files under ‘inst/doc’ ... OK
* 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 ... [61s/61s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
jarvisPatrick 5.702  0.121    5.84
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [26s/28s]
 [27s/28s] 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
  ‘/Users/biocbuild/bbs-2.13-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:202: warning: unused variable ‘id’
desc.cc:253: warning: comparison between signed and unsigned integer expressions
desc.cc:180: warning: unused variable ‘d’
desc.cc:218: warning: unused variable ‘Rf_ncols’
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-2.13-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	0.929	0.106	1.035
APset-class	0.841	0.105	0.946
FP-class	0.196	0.008	0.204
FPset-class	0.599	0.036	0.634
SDF-class	0.100	0.011	0.112
SDF2apcmp	0.047	0.002	0.049
SDFset-class	0.924	0.057	0.987
SDFset2SDF	0.220	0.017	0.238
SDFset2list	0.132	0.047	0.180
SDFstr-class	0.595	0.012	0.622
SMI-class	0.013	0.001	0.013
SMIset-class	0.039	0.005	0.044
addNewFeatures	4.444	0.174	4.650
ap	0.551	0.024	0.576
apfp	0.017	0.001	0.018
apset	0.019	0.002	0.021
apset2descdb	0.969	0.095	1.065
atomblock	0.374	0.028	0.407
atomcount	0.561	0.013	0.574
atomprop	0.011	0.002	0.012
atomsubset	0.063	0.002	0.065
batchByIndex	0.008	0.001	0.009
bondblock	0.341	0.020	0.360
bonds	0.061	0.011	0.071
bufferLines	0.006	0.003	0.008
bufferResultSet	0.010	0.003	0.013
byCluster	1.320	0.024	1.345
cid	0.099	0.006	0.105
cluster.sizestat	0.784	0.020	0.805
cluster.visualize	0.937	0.018	0.956
cmp.cluster	2.965	0.051	3.020
cmp.duplicated	0.071	0.009	0.079
cmp.parse	0.041	0.006	0.048
cmp.parse1	0.009	0.002	0.011
cmp.search	1.064	0.027	1.090
cmp.similarity	0.032	0.006	0.039
conMA	0.100	0.021	0.121
datablock	0.637	0.015	0.654
datablock2ma	0.070	0.007	0.077
db.explain	0.110	0.010	0.123
db.subset	0.121	0.008	0.128
dbTransaction	0.090	0.014	0.104
desc2fp	0.209	0.019	0.231
findCompounds	3.882	0.066	3.952
findCompoundsByName	0.650	0.021	0.673
fingerprintOB	0.019	0.002	0.020
fp2bit	1.470	0.119	1.592
fpSim	1.329	0.108	1.450
fromNNMatrix	1.431	0.009	1.440
genAPDescriptors	0.036	0.002	0.039
getCompoundNames	0.661	0.022	0.686
getCompounds	0.622	0.027	0.651
getIds	0.005	0.002	0.008
grepSDFset	0.096	0.003	0.100
groups	0.235	0.010	0.245
header	0.239	0.010	0.249
initDb	0.087	0.008	0.097
jarvisPatrick	5.702	0.121	5.840
listFeatures	0.625	0.020	0.646
loadSdf	4.236	0.086	4.327
makeUnique	0.059	0.005	0.064
nearestNeighbors	2.491	0.019	2.511
parBatchByIndex	0.014	0.006	0.020
plotStruc	0.381	0.011	0.392
propOB	0.012	0.003	0.015
pubchemFPencoding	0.009	0.004	0.012
read.AP	0.031	0.008	0.039
read.SDFindex	0.035	0.008	0.044
read.SDFset	0.888	0.006	0.895
read.SDFstr	1.477	0.004	1.480
read.SMIset	0.009	0.004	0.013
rings	0.815	0.016	0.831
sdf.subset	0.009	0.002	0.012
sdf.visualize	0.038	0.002	0.040
sdf2ap	0.858	0.121	0.981
sdf2list	0.042	0.015	0.057
sdf2smiles	0.008	0.002	0.009
sdf2str	0.060	0.012	0.072
sdfStream	0.036	0.009	0.045
sdfid	0.052	0.005	0.057
sdfsample	0.080	0.004	0.085
sdfstr2list	1.842	0.436	2.293
searchSim	0.010	0.005	0.014
searchString	0.012	0.004	0.017
selectInBatches	0.011	0.004	0.016
smiles2sdf	0.013	0.003	0.015
smisample	0.017	0.004	0.021
trimNeighbors	3.276	0.019	3.297
validSDF	0.052	0.002	0.054
view	0.161	0.008	0.169
write.SDF	0.357	0.009	0.365
write.SDFsplit	0.029	0.008	0.037
write.SMI	0.011	0.005	0.016