Package: ChemmineR

Version: 2.1.6

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.1.6.tar.gz

StartedAt: 2011-02-24 18:42:39 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:45:54 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 194.7 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/ChemmineR.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-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 ‘2.1.6’
* 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 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’
validSDF: no visible binding for global variable ‘sdfset’
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... 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	16.545	0.108	16.687
APset-class	16.113	0.120	16.247
SDF-class	0.080	0.004	0.084
SDF2apcmp	0.028	0.000	0.026
SDFset-class	0.816	0.040	0.857
SDFset2SDF	0.204	0.008	0.213
SDFset2list	0.088	0.024	0.112
SDFstr-class	0.416	0.004	0.418
ap	15.785	0.044	15.834
apset2descdb	16.113	0.108	16.242
atomblock	0.384	0.008	0.395
atomcount	0.432	0.004	0.438
atomprop	0.004	0.004	0.005
bondblock	0.328	0.008	0.338
cid	1.940	0.012	1.972
cluster.sizestat	5.456	0.012	6.009
cluster.visualize	5.785	0.012	6.579
cmp.cluster	7.792	0.068	8.691
cmp.duplicated	4.744	0.028	5.458
cmp.parse	4.781	0.012	5.690
cmp.parse1	0	0	0
cmp.search	5.644	0.008	6.335
cmp.similarity	4.780	0.012	5.499
datablock	0.744	0.012	0.755
datablock2ma	0.048	0.004	0.050
db.explain	4.733	0.032	5.383
db.subset	4.652	0.008	5.274
grepSDFset	0.072	0.000	0.073
header	0.380	0.000	0.379
makeUnique	0.088	0.000	0.086
plotStruc	0.276	0.000	0.276
read.SDFset	0.852	0.012	0.867
read.SDFstr	1.216	0.004	1.224
sdf.subset	4.932	0.020	5.705
sdf.visualize	4.761	0.020	8.755
sdf2ap	16.313	0.060	16.392
sdf2list	0.032	0.008	0.040
sdf2str	0.036	0.004	0.040
sdfid	0.044	0.000	0.048
sdfsample	0.096	0.000	0.096
sdfstr2list	0.896	0.272	1.169
validSDF	0.048	0.004	0.052
view	3.392	0.004	3.395
write.SDF	0.416	0.000	0.418