BioC 2.9: CHECK report for ChemmineR on liverpool

Package: ChemmineR

Version: 2.6.1

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.6.1.tar.gz

StartedAt: 2012-01-09 02:23:17 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 02:25:21 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 124.9 seconds

RetCode: 0

Status: OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/ChemmineR.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChemmineR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineR' version '2.6.1'
* 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 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 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	12.61	0.03	12.78
APset-class	12.67	0.05	12.86
SDF-class	0.09	0.00	0.27
SDF2apcmp	0.04	0.00	0.03
SDFset-class	0.67	0.00	0.67
SDFset2SDF	0.15	0.00	0.16
SDFset2list	0.10	0.02	0.11
SDFstr-class	0.5	0.0	0.5
ap	11.95	0.00	12.03
apset	0.02	0.00	0.01
apset2descdb	12.40	0.01	12.50
atomblock	0.28	0.00	0.28
atomcount	0.39	0.00	0.40
atomprop	0.02	0.00	0.01
atomsubset	0.05	0.00	0.05
bondblock	0.23	0.00	0.23
bonds	0.06	0.00	0.06
cid	1.44	0.00	1.46
cluster.sizestat	0.69	0.00	0.69
cluster.visualize	0.87	0.00	0.98
cmp.cluster	1.5	0.0	1.5
cmp.duplicated	0.11	0.00	0.11
cmp.parse	0.05	0.00	0.05
cmp.parse1	0	0	0
cmp.search	0.87	0.00	0.89
cmp.similarity	0.04	0.00	0.03
conMA	0.11	0.00	0.11
datablock	0.57	0.00	0.58
datablock2ma	0.07	0.00	0.06
db.explain	0.06	0.00	0.06
db.subset	0	0	0
fp2bit	0.81	0.03	0.84
fpSim	0.83	0.07	0.89
getIds	0	0	0
grepSDFset	0.08	0.00	0.08
groups	0.18	0.00	0.19
header	0.25	0.00	0.25
makeUnique	0.05	0.00	0.05
plotStruc	0.30	0.00	0.29
pubchemFPencoding	0	0	0
read.SDFset	0.83	0.00	0.83
read.SDFstr	1.25	0.00	1.25
rings	0.72	0.00	0.72
sdf.subset	0	0	0
sdf.visualize	0.03	0.00	0.03
sdf2ap	12.40	0.04	12.58
sdf2list	0.05	0.02	0.06
sdf2smiles	0	0	0
sdf2str	0.05	0.00	0.05
sdfid	0.04	0.00	0.05
sdfsample	0.08	0.00	0.07
sdfstr2list	1.20	0.08	1.30
searchSim	0	0	0
searchString	0	0	0
smiles2sdf	0	0	0
validSDF	0.07	0.00	0.06
view	2.5	0.0	2.5
write.SDF	0.23	0.01	0.27

Summary

Command output