Package: ChemmineR

Version: 2.9.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.9.0.tar.gz

StartedAt: 2012-06-20 22:43:53 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 22:47:07 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 194.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/ChemmineR.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '2.9.0'
* 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 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 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 'R/sim.R':
  found unlockBinding(".progress_bar_int_cnt",
    environment(.progress_bar))
.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 installed files from '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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/ChemmineR.Rcheck/00check.log'
for details.

* 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
** installing vignettes
   'ChemmineR.Rnw' 
** testing if installed package can be loaded

* DONE (ChemmineR)

name	user	system	elapsed
AP-class	20.346	0.282	20.970
APset-class	20.081	0.210	20.743
SDF-class	0.108	0.010	0.119
SDF2apcmp	0.031	0.002	0.034
SDFset-class	0.933	0.047	0.985
SDFset2SDF	0.224	0.012	0.236
SDFset2list	0.112	0.049	0.164
SDFstr-class	0.583	0.007	0.627
ap	19.467	0.053	19.855
apset	0.009	0.002	0.010
apset2descdb	19.958	0.160	20.236
atomblock	0.413	0.025	0.440
atomcount	0.588	0.009	0.607
atomprop	0.007	0.001	0.008
atomsubset	0.061	0.003	0.064
bondblock	0.377	0.017	0.396
bonds	0.066	0.004	0.070
cid	2.294	0.007	2.315
cluster.sizestat	1.102	0.018	1.124
cluster.visualize	1.424	0.021	1.521
cmp.cluster	2.402	0.040	2.466
cmp.duplicated	0.075	0.001	0.077
cmp.parse	0.052	0.003	0.056
cmp.parse1	0	0	0
cmp.search	1.361	0.026	1.405
cmp.similarity	0.042	0.003	0.046
conMA	0.120	0.019	0.139
datablock	0.790	0.014	0.817
datablock2ma	0.064	0.004	0.068
db.explain	0.075	0.008	0.084
db.subset	0.015	0.001	0.015
fp2bit	1.119	0.275	1.402
fpSim	1.064	0.275	1.359
getIds	0.001	0.000	0.000
grepSDFset	0.088	0.001	0.089
groups	0.267	0.008	0.279
header	0.292	0.009	0.301
makeUnique	0.045	0.001	0.047
plotStruc	0.421	0.009	0.440
pubchemFPencoding	0.005	0.001	0.006
read.SDFset	1.150	0.004	1.168
read.SDFstr	1.733	0.005	1.751
rings	1.002	0.013	1.021
sdf.subset	0	0	0
sdf.visualize	0.031	0.001	0.032
sdf2ap	20.117	0.160	20.574
sdf2list	0.041	0.014	0.056
sdf2smiles	0.000	0.000	0.001
sdf2str	0.045	0.006	0.051
sdfid	0.051	0.002	0.054
sdfsample	0.094	0.005	0.104
sdfstr2list	0.907	0.506	1.522
searchSim	0.000	0.000	0.001
searchString	0	0	0
smiles2sdf	0.000	0.001	0.000
validSDF	0.047	0.001	0.049
view	4.031	0.016	4.563
write.SDF	0.433	0.006	0.440