Package: ChemmineR

Version: 2.11.19

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.11.19.tar.gz

StartedAt: 2013-03-25 00:41:05 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:44:04 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 179.8 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 3.0.0 beta (2013-03-19 r62328)
* 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 ‘2.11.19’
* 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/15s] 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: findCompounds.Rd:27-29: Dropping empty section \details
prepare_Rd: findCompounds.Rd:30-36: Dropping empty section \value
prepare_Rd: findCompounds.Rd:43-45: Dropping empty section \note
prepare_Rd: findCompounds.Rd:40-42: Dropping empty section \author
prepare_Rd: findCompounds.Rd:37-39: Dropping empty section \references
prepare_Rd: findCompounds.Rd:49-51: Dropping empty section \seealso
prepare_Rd: findCompoundsByName.Rd:25-27: Dropping empty section \details
prepare_Rd: findCompoundsByName.Rd:28-34: Dropping empty section \value
prepare_Rd: findCompoundsByName.Rd:41-43: Dropping empty section \note
prepare_Rd: findCompoundsByName.Rd:38-40: Dropping empty section \author
prepare_Rd: findCompoundsByName.Rd:35-37: Dropping empty section \references
prepare_Rd: findCompoundsByName.Rd:47-49: Dropping empty section \seealso
prepare_Rd: getCompoundNames.Rd:22-24: Dropping empty section \details
prepare_Rd: getCompoundNames.Rd:25-31: Dropping empty section \value
prepare_Rd: getCompoundNames.Rd:38-40: Dropping empty section \note
prepare_Rd: getCompoundNames.Rd:35-37: Dropping empty section \author
prepare_Rd: getCompoundNames.Rd:32-34: Dropping empty section \references
prepare_Rd: getCompoundNames.Rd:44-46: Dropping empty section \seealso
prepare_Rd: getCompounds.Rd:25-27: Dropping empty section \details
prepare_Rd: getCompounds.Rd:28-34: Dropping empty section \value
prepare_Rd: getCompounds.Rd:41-43: Dropping empty section \note
prepare_Rd: getCompounds.Rd:38-40: Dropping empty section \author
prepare_Rd: getCompounds.Rd:35-37: Dropping empty section \references
prepare_Rd: getCompounds.Rd:47-49: Dropping empty section \seealso
prepare_Rd: initDb.Rd:21-23: Dropping empty section \details
prepare_Rd: initDb.Rd:24-30: Dropping empty section \value
prepare_Rd: initDb.Rd:37-39: Dropping empty section \note
prepare_Rd: initDb.Rd:34-36: Dropping empty section \author
prepare_Rd: initDb.Rd:31-33: Dropping empty section \references
prepare_Rd: initDb.Rd:43-45: 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: loadSdf.Rd:31-33: Dropping empty section \details
prepare_Rd: loadSdf.Rd:34-40: Dropping empty section \value
prepare_Rd: loadSdf.Rd:47-49: Dropping empty section \note
prepare_Rd: loadSdf.Rd:44-46: Dropping empty section \author
prepare_Rd: loadSdf.Rd:41-43: Dropping empty section \references
prepare_Rd: loadSdf.Rd:53-55: Dropping empty section \seealso
prepare_Rd: loadSmiles.Rd:25-27: Dropping empty section \details
prepare_Rd: loadSmiles.Rd:28-34: Dropping empty section \value
prepare_Rd: loadSmiles.Rd:41-43: Dropping empty section \note
prepare_Rd: loadSmiles.Rd:38-40: Dropping empty section \author
prepare_Rd: loadSmiles.Rd:35-37: Dropping empty section \references
prepare_Rd: loadSmiles.Rd:47-49: Dropping empty section \seealso
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 ... [61s/62s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
jarvisPatrick 9.713  0.768  10.542
trimNeighbors 5.616  0.008   5.646
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [29s/30s]
 [30s/30s] 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
   ‘ChemmineR.Rnw’ 
** testing if installed package can be loaded
* DONE (ChemmineR)

name	user	system	elapsed
AP-class	2.212	0.072	2.406
APset-class	2.012	0.092	2.109
FP-class	0.168	0.016	0.184
FPset-class	1.052	0.016	1.106
SDF-class	0.120	0.004	0.124
SDF2apcmp	0.048	0.000	0.049
SDFset-class	0.924	0.060	0.995
SDFset2SDF	0.220	0.012	0.233
SDFset2list	0.248	0.020	0.267
SDFstr-class	0.592	0.016	0.606
ap	1.304	0.016	1.324
apfp	0.032	0.000	0.032
apset	0.032	0.000	0.033
apset2descdb	1.864	0.076	1.939
atomblock	0.508	0.032	0.541
atomcount	0.588	0.000	0.585
atomprop	0.016	0.000	0.019
atomsubset	0.076	0.000	0.075
batchByIndex	0.020	0.004	0.024
bondblock	0.432	0.016	0.448
bonds	0.080	0.020	0.102
bufferLines	0.016	0.004	0.023
bufferResultSet	0.016	0.012	0.025
cid	0.272	0.004	0.276
cluster.sizestat	1.120	0.008	1.128
cluster.visualize	1.161	0.020	1.180
cmp.cluster	3.872	0.032	3.922
cmp.duplicated	0.124	0.008	0.131
cmp.parse	0.052	0.016	0.068
cmp.parse1	0.008	0.000	0.010
cmp.search	1.252	0.008	1.262
cmp.similarity	0.052	0.004	0.058
conMA	0.116	0.004	0.121
datablock	0.956	0.008	0.967
datablock2ma	0.092	0.020	0.111
db.explain	0.104	0.000	0.106
db.subset	0.032	0.000	0.032
desc2fp	0.476	0.012	0.494
findCompounds	0.052	0.000	0.054
findCompoundsByName	0.028	0.000	0.024
fp2bit	1.792	0.008	1.803
fpSim	1.752	0.104	1.870
getCompoundNames	0.020	0.000	0.019
getCompounds	0.048	0.000	0.046
getIds	0.012	0.000	0.012
grepSDFset	0.112	0.008	0.118
groups	0.252	0.012	0.261
header	0.344	0.008	0.355
initDb	0.024	0.008	0.034
jarvisPatrick	9.713	0.768	10.542
loadSdf	0.060	0.000	0.058
loadSmiles	0.016	0.000	0.018
makeUnique	0.068	0.000	0.069
nearestNeighbors	4.648	0.004	4.654
plotStruc	0.480	0.000	0.483
pubchemFPencoding	0.008	0.004	0.013
read.AP	0.056	0.004	0.058
read.SDFindex	0.172	0.008	0.181
read.SDFset	1.156	0.000	1.158
read.SDFstr	2	0	2
rings	1.000	0.004	1.003
sdf.subset	0.012	0.000	0.012
sdf.visualize	0.036	0.004	0.044
sdf2ap	1.624	0.068	1.707
sdf2list	0.056	0.004	0.059
sdf2smiles	0.012	0.004	0.018
sdf2str	0.064	0.000	0.064
sdfStream	0.064	0.004	0.070
sdfid	0.068	0.012	0.081
sdfsample	0.092	0.004	0.094
sdfstr2list	1.120	0.248	1.366
searchSim	0.024	0.000	0.022
searchString	0.016	0.004	0.017
selectInBatches	0.024	0.000	0.024
smiles2sdf	0.016	0.000	0.016
trimNeighbors	5.616	0.008	5.646
validSDF	0.076	0.004	0.078
view	0.360	0.004	0.378
write.SDF	0.392	0.004	0.398
write.SDFsplit	0.164	0.004	0.167