Package: ChemmineR

Version: 2.5.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.5.0.tar.gz

StartedAt: 2011-06-22 02:03:52 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 02:11:38 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 465.6 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/ChemmineR.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘2.5.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘ChemmineR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
.data.frame.to.str: no visible binding for global variable ‘string’
.gen_atom_pair: no visible global function definition for
  ‘Descriptors_get_len’
.gen_atom_pair: no visible global function definition for
  ‘Descriptors_get_descriptor’
.parse: no visible global function definition for ‘Descriptors’
.parse: no visible global function definition for
  ‘Descriptors_parse_sdf’
cmp.parse: no visible global function definition for ‘batch_parse’
cmp.parse1: no visible global function definition for
  ‘delete_Descriptors’
datablock2ma: no visible binding for global variable ‘sdfset’
sdf_to_desc: no visible global function definition for
  ‘delete_Descriptors’
sdfs_to_desc: no visible global function definition for ‘batch_parse’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ calls not declared from:
  ‘gplots’ ‘scatterplot3d’
* 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

* installing *source* package ‘ChemmineR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for "plot" from package "graphics" in package “ChemmineR”
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘ChemmineR.Rnw’ 
** testing if installed package can be loaded

* DONE (ChemmineR)

name	user	system	elapsed
AP-class	20.276	0.205	21.527
APset-class	20.018	0.186	21.567
SDF-class	0.145	0.010	0.198
SDF2apcmp	0.053	0.002	0.087
SDFset-class	1.147	0.045	1.308
SDFset2SDF	0.334	0.014	0.360
SDFset2list	0.170	0.051	0.456
SDFstr-class	0.656	0.005	0.733
ap	19.387	0.085	22.399
apset	0.020	0.003	0.379
apset2descdb	19.440	0.140	66.517
atomblock	0.456	0.028	0.525
atomcount	0.595	0.011	0.634
atomprop	0.008	0.001	0.107
bondblock	0.392	0.017	0.419
cid	2.303	0.009	2.437
cluster.sizestat	1.195	0.019	1.298
cluster.visualize	1.296	0.023	1.842
cmp.cluster	2.574	0.046	2.877
cmp.duplicated	0.085	0.002	0.132
cmp.parse	0.075	0.003	0.097
cmp.parse1	0.000	0.000	0.001
cmp.search	1.503	0.027	1.616
cmp.similarity	0.047	0.002	0.051
conMA	0.147	0.017	0.177
datablock	0.933	0.016	1.035
datablock2ma	0.105	0.003	0.111
db.explain	0.154	0.009	0.242
db.subset	0.014	0.001	0.045
fp2bit	1.175	0.258	1.557
fpSim	1.145	0.266	1.588
getIds	0.001	0.001	0.000
grepSDFset	0.166	0.002	0.179
header	0.306	0.006	0.326
makeUnique	0.070	0.001	0.099
plotStruc	0.456	0.006	0.528
pubchemFPencoding	0.007	0.001	0.068
read.SDFset	1.290	0.006	1.359
read.SDFstr	1.884	0.007	1.989
sdf.subset	0	0	0
sdf.visualize	0.052	0.002	0.056
sdf2ap	19.966	0.169	20.960
sdf2list	0.073	0.015	0.100
sdf2smiles	0.000	0.000	0.001
sdf2str	0.093	0.007	0.174
sdfid	0.069	0.002	0.079
sdfsample	0.144	0.005	0.163
sdfstr2list	3.245	0.544	5.782
searchSim	0.000	0.000	0.001
searchString	0.001	0.000	0.000
smiles2sdf	0.000	0.000	0.001
validSDF	0.073	0.003	0.076
view	3.988	0.015	4.223
write.SDF	0.558	0.006	0.771