BioC 2.9: CHECK report for ChemmineR on pitt

Package: ChemmineR

Version: 2.5.3

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.5.3.tar.gz

StartedAt: 2011-07-07 02:14:08 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:17:23 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 194.8 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) (2011-06-22 r56208)
* 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 '2.5.3'
* 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' ... 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

* 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 ...
*** tangling vignette sources ...
   'ChemmineR.Rnw' 
** testing if installed package can be loaded

* DONE (ChemmineR)

name	user	system	elapsed
AP-class	20.540	0.197	20.973
APset-class	20.229	0.183	20.959
SDF-class	0.149	0.010	0.160
SDF2apcmp	0.054	0.003	0.057
SDFset-class	1.205	0.046	1.268
SDFset2SDF	0.318	0.012	0.332
SDFset2list	0.139	0.050	0.192
SDFstr-class	0.634	0.006	0.643
ap	19.722	0.086	20.175
apset	0.018	0.002	0.025
apset2descdb	20.183	0.158	20.517
atomblock	0.420	0.026	0.450
atomcount	0.609	0.008	0.628
atomprop	0.008	0.001	0.008
bondblock	0.400	0.017	0.423
bonds	0.102	0.004	0.107
cid	2.321	0.011	2.349
cluster.sizestat	1.261	0.016	1.287
cluster.visualize	1.325	0.019	1.386
cmp.cluster	2.660	0.045	2.733
cmp.duplicated	0.084	0.002	0.087
cmp.parse	0.077	0.003	0.080
cmp.parse1	0.000	0.000	0.001
cmp.search	1.520	0.027	1.566
cmp.similarity	0.049	0.003	0.051
conMA	0.148	0.016	0.165
datablock	0.950	0.014	0.983
datablock2ma	0.086	0.003	0.088
db.explain	0.084	0.008	0.093
db.subset	0.014	0.001	0.016
fp2bit	1.213	0.279	1.547
fpSim	1.168	0.270	1.452
getIds	0.000	0.000	0.001
grepSDFset	0.109	0.002	0.112
header	0.309	0.008	0.318
makeUnique	0.120	0.002	0.122
plotStruc	0.506	0.008	0.525
pubchemFPencoding	0.006	0.001	0.006
read.SDFset	1.202	0.012	1.223
read.SDFstr	1.802	0.006	1.837
sdf.subset	0.000	0.000	0.001
sdf.visualize	0.054	0.001	0.055
sdf2ap	20.128	0.175	20.516
sdf2list	0.066	0.017	0.083
sdf2smiles	0.000	0.000	0.001
sdf2str	0.073	0.007	0.080
sdfid	0.066	0.002	0.068
sdfsample	0.141	0.005	0.147
sdfstr2list	0.889	0.512	1.431
searchSim	0	0	0
searchString	0.001	0.001	0.000
smiles2sdf	0.000	0.000	0.001
validSDF	0.070	0.002	0.072
view	4.106	0.019	4.198
write.SDF	0.566	0.007	0.579

Summary

Command output