Package: ChemmineR

Version: 2.8.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.8.1.tar.gz

StartedAt: 2012-09-23 23:39:56 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:42:48 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 171.8 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/ChemmineR.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '2.8.1'
* 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-2.10-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	22.490	0.127	22.617
APset-class	16.050	0.093	16.144
SDF-class	0.074	0.007	0.082
SDF2apcmp	0.025	0.001	0.028
SDFset-class	0.660	0.032	0.715
SDFset2SDF	0.162	0.008	0.170
SDFset2list	0.081	0.034	0.115
SDFstr-class	0.392	0.003	0.395
ap	14.731	0.027	14.758
apset	0.010	0.001	0.012
apset2descdb	16.563	0.129	16.693
atomblock	0.437	0.027	0.465
atomcount	0.550	0.008	0.559
atomprop	0.007	0.001	0.007
atomsubset	0.067	0.002	0.070
bondblock	0.323	0.016	0.339
bonds	0.130	0.004	0.133
cid	2.369	0.003	2.371
cluster.sizestat	0.873	0.011	0.884
cluster.visualize	1.103	0.013	1.117
cmp.cluster	1.909	0.027	1.936
cmp.duplicated	0.053	0.001	0.054
cmp.parse	0.042	0.003	0.044
cmp.parse1	0	0	0
cmp.search	1.164	0.015	1.179
cmp.similarity	0.028	0.001	0.031
conMA	0.080	0.012	0.093
datablock	0.516	0.008	0.525
datablock2ma	0.047	0.002	0.049
db.explain	0.091	0.006	0.096
db.subset	0.004	0.001	0.006
fp2bit	0.822	0.187	1.015
fpSim	0.782	0.173	0.956
getIds	0	0	0
grepSDFset	0.060	0.001	0.061
groups	0.232	0.006	0.239
header	0.170	0.004	0.174
makeUnique	0.076	0.001	0.076
plotStruc	0.350	0.008	0.358
pubchemFPencoding	0.003	0.001	0.004
read.SDFset	0.809	0.001	0.810
read.SDFstr	1.793	0.002	1.795
rings	1.206	0.011	1.217
sdf.subset	0.000	0.001	0.001
sdf.visualize	0.036	0.001	0.037
sdf2ap	18.487	0.090	18.578
sdf2list	0.032	0.011	0.042
sdf2smiles	0.000	0.000	0.001
sdf2str	0.036	0.005	0.041
sdfid	0.038	0.001	0.040
sdfsample	0.109	0.005	0.114
sdfstr2list	0.985	0.523	1.521
searchSim	0	0	0
searchString	0	0	0
smiles2sdf	0.000	0.000	0.001
validSDF	0.051	0.001	0.052
view	4.551	0.008	4.559
write.SDF	0.447	0.005	0.452