Package: ChemmineR

Version: 2.5.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.5.0.tar.gz

StartedAt: 2011-05-09 13:51:17 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:55:15 -0700 (Mon, 09 May 2011)

EllapsedTime: 238.1 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/ChemmineR.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘2.5.0’
* 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘ChemmineR.pdf’ from 1250Kb to 552Kb
  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 ...
*** tangling vignette sources ...
   ‘ChemmineR.Rnw’ 
** testing if installed package can be loaded

* DONE (ChemmineR)

name	user	system	elapsed
AP-class	29.424	0.196	30.522
APset-class	29.106	0.164	29.641
SDF-class	0.141	0.010	0.152
SDF2apcmp	0.054	0.003	0.057
SDFset-class	1.117	0.046	1.170
SDFset2SDF	0.371	0.013	0.384
SDFset2list	0.168	0.048	0.218
SDFstr-class	0.635	0.006	0.652
ap	28.629	0.068	28.870
apset	0.017	0.002	0.019
apset2descdb	29.108	0.163	29.447
atomblock	0.456	0.026	0.482
atomcount	0.590	0.006	0.597
atomprop	0.008	0.001	0.009
bondblock	0.356	0.015	0.376
cid	3.388	0.009	3.432
cluster.sizestat	1.153	0.017	1.173
cluster.visualize	1.330	0.020	1.356
cmp.cluster	2.635	0.044	2.704
cmp.duplicated	0.080	0.001	0.082
cmp.parse	0.074	0.002	0.078
cmp.parse1	0	0	0
cmp.search	1.467	0.027	1.508
cmp.similarity	0.051	0.003	0.062
conMA	0.145	0.016	0.169
datablock	0.900	0.015	0.948
datablock2ma	0.104	0.003	0.108
db.explain	0.186	0.008	0.194
db.subset	0.014	0.001	0.014
fp2bit	1.170	0.261	1.454
fpSim	1.139	0.267	1.443
getIds	0	0	0
grepSDFset	0.122	0.002	0.124
header	0.367	0.007	0.375
makeUnique	0.062	0.001	0.073
plotStruc	0.451	0.006	0.457
pubchemFPencoding	0.006	0.001	0.006
read.SDFset	1.286	0.003	1.295
read.SDFstr	1.846	0.006	1.858
sdf.subset	0.000	0.001	0.000
sdf.visualize	0.054	0.001	0.055
sdf2ap	29.394	0.166	29.828
sdf2list	0.072	0.015	0.088
sdf2smiles	0.000	0.001	0.000
sdf2str	0.092	0.006	0.098
sdfid	0.071	0.002	0.073
sdfsample	0.146	0.005	0.151
sdfstr2list	3.241	0.524	3.811
searchSim	0.000	0.000	0.001
searchString	0	0	0
smiles2sdf	0.000	0.001	0.000
validSDF	0.086	0.002	0.088
view	5.848	0.017	5.887
write.SDF	0.533	0.006	0.540