Package: ChemmineR

Version: 2.4.4

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.4.4.tar.gz

StartedAt: 2011-10-20 14:09:18 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:13:17 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 239.6 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 2.13.2 (2011-09-30)
* 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 '2.4.4'
* checking package namespace 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 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
.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 ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'ChemmineR.pdf' from 1292Kb to 620Kb
  consider running tools::compactPDF() on these files
* 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 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	29.289	0.185	29.808
APset-class	29.035	0.164	29.450
SDF-class	0.139	0.010	0.150
SDF2apcmp	0.056	0.002	0.058
SDFset-class	1.171	0.045	1.228
SDFset2SDF	0.303	0.012	0.318
SDFset2list	0.132	0.048	0.181
SDFstr-class	0.643	0.006	0.654
ap	28.687	0.073	29.007
apset	0.021	0.002	0.022
apset2descdb	29.058	0.158	29.444
atomblock	0.396	0.025	0.424
atomcount	0.593	0.008	0.603
atomprop	0.007	0.001	0.008
bondblock	0.391	0.017	0.410
bonds	0.096	0.004	0.100
cid	3.407	0.011	3.435
cluster.sizestat	1.159	0.019	1.193
cluster.visualize	1.348	0.020	1.374
cmp.cluster	2.643	0.040	2.694
cmp.duplicated	0.081	0.002	0.087
cmp.parse	0.071	0.003	0.074
cmp.parse1	0	0	0
cmp.search	1.445	0.023	1.472
cmp.similarity	0.047	0.002	0.050
conMA	0.144	0.016	0.160
datablock	0.854	0.013	0.874
datablock2ma	0.085	0.003	0.088
db.explain	0.085	0.007	0.093
db.subset	0.016	0.001	0.017
fp2bit	1.208	0.299	1.528
fpSim	1.187	0.314	1.519
getIds	0.000	0.000	0.001
grepSDFset	0.118	0.002	0.122
groups	0.317	0.008	0.326
header	0.366	0.008	0.375
makeUnique	0.065	0.001	0.066
plotStruc	0.545	0.006	0.555
pubchemFPencoding	0.006	0.001	0.007
read.SDFset	1.229	0.004	1.237
read.SDFstr	1.812	0.006	1.830
rings	1.242	0.012	1.262
sdf.subset	0.000	0.000	0.001
sdf.visualize	0.053	0.001	0.054
sdf2ap	29.083	0.176	29.425
sdf2list	0.066	0.015	0.081
sdf2smiles	0.001	0.000	0.000
sdf2str	0.065	0.006	0.070
sdfid	0.069	0.001	0.070
sdfsample	0.139	0.004	0.144
sdfstr2list	0.873	0.487	1.371
searchSim	0.000	0.000	0.001
searchString	0	0	0
smiles2sdf	0.000	0.000	0.001
validSDF	0.085	0.001	0.087
view	5.890	0.020	6.028
write.SDF	0.510	0.005	0.524