Package: ChemmineR

Version: 2.2.14

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.2.14.tar.gz

StartedAt: 2011-03-17 15:55:46 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 15:59:54 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 248.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/ChemmineR.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ChemmineR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineR' version '2.2.14'
* 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 examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'ChemmineR' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "plot" in "ChemmineR"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ChemmineR)

name	user	system	elapsed
AP-class	21.014	0.130	21.145
APset-class	21.579	0.143	21.723
SDF-class	0.106	0.007	0.114
SDF2apcmp	0.039	0.001	0.041
SDFset-class	0.841	0.032	0.873
SDFset2SDF	0.275	0.010	0.284
SDFset2list	0.105	0.034	0.138
SDFstr-class	0.444	0.004	0.448
ap	21.187	0.073	21.261
apset	0.012	0.001	0.013
apset2descdb	21.929	0.143	22.072
atomblock	0.300	0.019	0.319
atomcount	0.454	0.010	0.463
atomprop	0.004	0.001	0.005
bondblock	0.280	0.012	0.292
cid	2.447	0.008	2.455
cluster.sizestat	0.855	0.007	0.863
cluster.visualize	0.991	0.010	1.002
cmp.cluster	1.972	0.018	1.990
cmp.duplicated	0.056	0.001	0.057
cmp.parse	0.056	0.001	0.058
cmp.parse1	0	0	0
cmp.search	1.098	0.014	1.112
cmp.similarity	0.035	0.001	0.035
datablock	0.656	0.012	0.669
datablock2ma	0.092	0.004	0.095
db.explain	0.059	0.005	0.064
db.subset	0.013	0.002	0.015
fp2bit	0.806	0.055	0.862
fpSim	0.837	0.047	0.884
getIds	0.026	0.003	7.672
grepSDFset	0.077	0.001	0.078
header	0.260	0.006	0.266
makeUnique	0.046	0.000	0.046
plotStruc	0.360	0.004	0.364
pubchemFPencoding	0.005	0.000	0.004
read.SDFset	0.840	0.002	0.841
read.SDFstr	1.330	0.001	1.331
sdf.subset	0	0	0
sdf.visualize	0.044	0.001	0.045
sdf2ap	21.832	0.089	21.922
sdf2list	0.048	0.010	0.058
sdf2smiles	0.051	0.001	0.367
sdf2str	0.052	0.005	0.057
sdfid	0.052	0.005	0.056
sdfsample	0.113	0.005	0.119
sdfstr2list	0.703	0.336	1.040
searchString	0.817	0.009	30.269
searchSub	0.129	0.005	40.758
smiles2sdf	0.010	0.000	0.215
validSDF	0.093	0.001	0.094
view	4.364	0.012	4.376
write.SDF	0.379	0.005	0.385