BioC 2.12: CHECK report for ChemmineR on george2

Package: ChemmineR

Version: 2.12.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.12.3.tar.gz

StartedAt: 2013-10-09 00:48:07 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:51:44 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 217.0 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ChemmineR.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘2.12.3’
* 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 ... [14s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* 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’
* checking Rd files ... NOTE
prepare_Rd: batchByIndex.Rd:27-29: Dropping empty section \details
prepare_Rd: batchByIndex.Rd:30-36: Dropping empty section \value
prepare_Rd: batchByIndex.Rd:43-45: Dropping empty section \note
prepare_Rd: batchByIndex.Rd:40-42: Dropping empty section \author
prepare_Rd: batchByIndex.Rd:37-39: Dropping empty section \references
prepare_Rd: batchByIndex.Rd:49-51: Dropping empty section \seealso
prepare_Rd: bufferLines.Rd:25-27: Dropping empty section \details
prepare_Rd: bufferLines.Rd:28-34: Dropping empty section \value
prepare_Rd: bufferLines.Rd:41-43: Dropping empty section \note
prepare_Rd: bufferLines.Rd:38-40: Dropping empty section \author
prepare_Rd: bufferLines.Rd:35-37: Dropping empty section \references
prepare_Rd: bufferLines.Rd:47-49: Dropping empty section \seealso
prepare_Rd: bufferResultSet.Rd:28-30: Dropping empty section \details
prepare_Rd: bufferResultSet.Rd:31-37: Dropping empty section \value
prepare_Rd: bufferResultSet.Rd:44-46: Dropping empty section \note
prepare_Rd: bufferResultSet.Rd:41-43: Dropping empty section \author
prepare_Rd: bufferResultSet.Rd:38-40: Dropping empty section \references
prepare_Rd: bufferResultSet.Rd:50-52: Dropping empty section \seealso
prepare_Rd: jarvisPatrick_c.Rd:40-42: Dropping empty section \details
prepare_Rd: jarvisPatrick_c.Rd:43-49: Dropping empty section \value
prepare_Rd: jarvisPatrick_c.Rd:56-58: Dropping empty section \note
prepare_Rd: jarvisPatrick_c.Rd:53-55: Dropping empty section \author
prepare_Rd: jarvisPatrick_c.Rd:50-52: Dropping empty section \references
prepare_Rd: jarvisPatrick_c.Rd:62-64: Dropping empty section \seealso
prepare_Rd: jarvisPatrick_c.Rd:65-67: Dropping empty section \examples
prepare_Rd: selectInBatches.Rd:30-32: Dropping empty section \details
prepare_Rd: selectInBatches.Rd:33-39: Dropping empty section \value
prepare_Rd: selectInBatches.Rd:46-48: Dropping empty section \note
prepare_Rd: selectInBatches.Rd:43-45: Dropping empty section \author
prepare_Rd: selectInBatches.Rd:40-42: Dropping empty section \references
prepare_Rd: selectInBatches.Rd:52-54: Dropping empty section \seealso
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.12-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 examples ... [83s/88s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
jarvisPatrick  9.517  0.388  10.690
trimNeighbors  5.640  0.036   6.375
addNewFeatures 5.572  0.048   5.768
loadSdf        4.972  0.032   5.237
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [29s/32s]
 [30s/32s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -fpic  -g -O2  -Wall -c DisjointSets.cpp -o DisjointSets.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -fpic  -g -O2  -Wall -c desc.cc -o desc.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -fpic  -g -O2  -Wall -c formats.cc -o formats.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -fpic  -g -O2  -Wall -c molecule.cc -o molecule.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -fpic  -g -O2  -Wall -c script.cc -o script.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -fpic  -g -O2  -Wall -c similarity.cc -o similarity.o
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-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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	2.132	0.104	2.486
APset-class	1.884	0.080	2.548
FP-class	0.296	0.004	0.298
FPset-class	0.964	0.020	1.090
SDF-class	0.140	0.000	0.142
SDF2apcmp	0.068	0.000	0.075
SDFset-class	1.060	0.044	1.113
SDFset2SDF	0.272	0.004	0.276
SDFset2list	0.252	0.020	0.271
SDFstr-class	0.644	0.004	0.661
addNewFeatures	5.572	0.048	5.768
ap	1.317	0.016	1.477
apfp	0.020	0.004	0.023
apset	0.036	0.000	0.036
apset2descdb	1.708	0.072	2.135
atomblock	0.480	0.016	0.554
atomcount	0.568	0.012	0.638
atomprop	0.016	0.004	0.021
atomsubset	0.060	0.004	0.067
batchByIndex	0.02	0.00	0.02
bondblock	0.604	0.008	0.688
bonds	0.076	0.000	0.077
bufferLines	0.016	0.000	0.016
bufferResultSet	0.020	0.000	0.025
byCluster	1.744	0.004	1.907
cid	0.336	0.004	0.337
cluster.sizestat	1.00	0.00	1.02
cluster.visualize	1.204	0.008	1.214
cmp.cluster	4.072	0.028	4.149
cmp.duplicated	0.108	0.012	0.122
cmp.parse	0.052	0.000	0.051
cmp.parse1	0.008	0.000	0.007
cmp.search	1.320	0.012	1.389
cmp.similarity	0.052	0.000	0.050
conMA	0.112	0.008	0.121
datablock	1.040	0.012	1.053
datablock2ma	0.112	0.000	0.112
db.explain	0.116	0.000	0.116
db.subset	0.164	0.004	0.168
desc2fp	0.421	0.008	0.429
findCompounds	4.796	0.016	4.823
findCompoundsByName	0.820	0.024	0.853
fp2bit	1.980	0.124	2.113
fpSim	2.020	0.072	2.110
fromNNMatrix	2.004	0.000	2.157
getCompoundNames	0.752	0.012	0.878
getCompounds	0.680	0.008	0.763
getIds	0.012	0.000	0.013
grepSDFset	0.124	0.000	0.138
groups	0.384	0.008	0.418
header	0.236	0.012	0.317
initDb	0.06	0.00	0.06
jarvisPatrick	9.517	0.388	10.690
loadSdf	4.972	0.032	5.237
makeUnique	0.064	0.008	0.103
nearestNeighbors	4.317	0.004	4.382
plotStruc	0.496	0.012	0.530
pubchemFPencoding	0.012	0.000	0.013
read.AP	0.048	0.000	0.050
read.SDFindex	0.196	0.012	0.210
read.SDFset	1.204	0.008	1.298
read.SDFstr	2.020	0.008	2.048
rings	1.048	0.016	1.069
sdf.subset	0.012	0.000	0.014
sdf.visualize	0.040	0.000	0.039
sdf2ap	1.748	0.068	2.102
sdf2list	0.040	0.016	0.059
sdf2smiles	0.02	0.00	0.02
sdf2str	0.056	0.012	0.067
sdfStream	0.08	0.00	0.08
sdfid	0.28	0.00	0.28
sdfsample	0.108	0.008	0.117
sdfstr2list	1.124	0.268	1.409
searchSim	0.024	0.000	0.027
searchString	0.020	0.000	0.019
selectInBatches	0.008	0.016	0.026
smiles2sdf	0.008	0.004	0.013
trimNeighbors	5.640	0.036	6.375
validSDF	0.229	0.008	0.234
view	0.332	0.004	0.334
write.SDF	0.436	0.012	0.463
write.SDFsplit	0.028	0.008	0.039