Package: ChemmineR

Version: 2.1.6

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.1.6.tar.gz

StartedAt: 2011-02-24 15:20:34 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 15:24:18 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 224.4 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) (2011-01-10 r53950)
* 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 '2.1.6'
* 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 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'
validSDF: no visible binding for global variable 'sdfset'
* 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 data for non-ASCII characters ... 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	20.006	0.085	20.092
APset-class	19.752	0.093	19.847
SDF-class	0.104	0.006	0.110
SDF2apcmp	0.039	0.002	0.040
SDFset-class	0.832	0.029	0.861
SDFset2SDF	0.262	0.009	0.272
SDFset2list	0.099	0.031	0.130
SDFstr-class	0.440	0.003	0.444
ap	19.505	0.030	19.536
apset2descdb	20.038	0.093	20.131
atomblock	0.296	0.017	0.313
atomcount	0.456	0.007	0.462
atomprop	0.005	0.001	0.005
bondblock	0.283	0.009	0.293
cid	2.318	0.003	2.321
cluster.sizestat	6.262	0.032	6.866
cluster.visualize	6.510	0.027	6.888
cmp.cluster	9.150	0.041	9.536
cmp.duplicated	5.683	0.019	6.053
cmp.parse	5.487	0.017	5.887
cmp.parse1	0.001	0.000	0.000
cmp.search	6.515	0.028	7.060
cmp.similarity	5.574	0.016	6.014
datablock	0.706	0.020	0.726
datablock2ma	0.064	0.002	0.066
db.explain	5.618	0.018	5.991
db.subset	5.699	0.012	6.061
grepSDFset	0.083	0.001	0.084
header	0.326	0.008	0.335
makeUnique	0.052	0.001	0.053
plotStruc	0.363	0.004	0.368
read.SDFset	0.949	0.004	0.953
read.SDFstr	1.334	0.003	1.337
sdf.subset	5.858	0.016	6.382
sdf.visualize	5.750	0.028	9.512
sdf2ap	20.491	0.096	20.588
sdf2list	0.048	0.010	0.057
sdf2str	0.049	0.004	0.053
sdfid	0.053	0.001	0.053
sdfsample	0.139	0.003	0.141
sdfstr2list	0.677	0.324	1.002
validSDF	0.054	0.001	0.055
view	3.972	0.012	3.984
write.SDF	0.409	0.004	0.413